Muktol

I would be interested in a short report after your tests on Saturday.
And I would tweak the manabase a little bit before that, you have 9 Forests and 7 Swamps, but a 3:1 ratio leaning toward green cards.

Going over the deck again, I think the part I don't really like is [[Lumberknot]].
[[Lumberknot]] requires something to die to get stronger, but you don't have any cards that could let you effectively sacrifice anything for [[Lumberknot]]. Itself is not strong enough to block creatures, so you might have a problem with aggro decks. So basically it's a 1/1 hexproof for 4 mana, with an ability that will trigger very rarely.
I would still take a look at [[Dungrove Elder]] as he doesn't need the +1/+1 counters to be of use, but has hexproof and can be combined with Hydra's Growth. And you even wouldn't have to change the title as the Elder is a Treefolk ;)
Another thing that just comes to my mind would be evasion of one sort or another: [[Evolution Charm]], [[Rancor]] or something like [[Zephyr Boots]]

Well the "standard" enchantment decks normally are built around 1/1 hexproof creatures with as many cheap but effective auras as you can pack into a deck. Very fast, very explosive.
The problem I see with [[Homicidal Seclusion]] is that hexproof creatures, even if they are only 1/1's, do not die that easily, especially if your opponent sees that you have a [[Homicidal Seclusion]] on the field.
If you want to stick with [[Hydra's Growth]] then [[Forced Adaptation]] could be worth a look. As you decide which trigger resolves first, this could help you to built up counters more quickly.
I would also trade [[Season of Growth]] for something that gives you cards when you need it, like [[Harmonize]] or [[Village Rites]]. The last one could also take care of any creatures you have that prevent you from getting [[Homicidal Seclusion]]'s bonus.

+1
Your way of building a hexproof deck is different from the "standard", which can be a good thing. It would be nice, if you could write up a short description why you did built the deck this way and why you did differ from the standard builds.
Personally I would either make this deck mono green or add white as second colour. I would also try to get more constancy into the deck, meaning less 1 and 2-offs but focus more on 4 copies of a card.
[[Homicidal Seclusion]] is to slow and surviving long enough to get the maximum use out of [[Hydra's Growth]] could also be difficult, if your toughest creature is a 4/4...that you only have 3 times in your deck.
[[Dungrove Elder]] would be a great creature in mono green, and a pain in the ass for control decks. [[Rancor]] is always a great card as no matter what you enchant with it, if the creature dies, it comes back and can be re-used.
White would give access to things like [[Unflinching Courage]] as well as some more "classic" enchantment cards: [[Ethereal Armor]], [[Hyena Umbra]], [[Spirit Mantle]]
[[Helm of the Gods]] would be a weaker but colourless version of [[Ethereal Armor]]

The last mill deck I've tried to build in pauper used the following mill cards:
4 [[Mind Sculpt]], 4 [[Tome Scour]], 4 [[Dream Twist]], 4 [[Thought Scour]], 4 [[Merfolk Secretkeeper // Venture Deeper]], and 4 [[Jace's Erasure]]. The rest was either draw or removal. Against mono black control the deck did OK, as my MBC-testdeck is more focused on creature-removal than discard and not really fast. The problems where the aggro decks: mono green Stompy, mono white heroic, W/R humans, and so on...they all are simply to fast before the deck runs out of power (aka mill-cards).
This time I wanted to focus on defence and mill more slowly, but with [[Jace's Erasure]] being my only mill-option this is very fragile. I really would like to get a mill-deck working that is playable, but in pauper this seems to be very hard.

By the way, could you lend me a helping hand with this one:
https://www.mtgvault.com/muktol/decks/ub-pauper-defensive-mill/
It's a pauper deck, so commons only. I've tried some approaches to the mill-strategy using pauper, but have gotten to no result that did what I wanted: survive and mill.

Is this deck built for single- or multiplayer games?
"Some of the combos in the deck"... The only "combo" I see would be [[Underworld Breach]]+[[Runaway Steam-Kin]]+[[Guttersnipe]]+a graveyard full of spells, which is a contrast to your strategy of "waiting for the right moment"...which would mean to me that the graveyard won't be as full as you need it. Rather unlikely that you will be able to play this, as your opponents will simply remove one part of the combo or you won't even get all the pieces together. If I've overlooked something (which is rather possible) please explain and add the a description how the combos work into your description.

+1
The lands wouldn't be destroyed when you cast [[All is dust]], as they are colourless:
105.2. An object can be one or more of the five colors, or it can be no color at all. An object is the color or colors of the mana symbols in its mana cost, regardless of the color of its frame. An object’s color or colors may also be defined by a color indicator or a characteristic-defining ability.

[[Coat of Arms]] and [[Sarcomite Myr]] have no costs ($) as you've selected a version that has not been priced yet.

[[Metallic Mimic]] could be an idea here, and if you're willing to include white then [[Tempered Steel]] and [[Myrsmith]] could also be worth a look.

Personally I would try to include some carddraw and/ or the ability to sink your excess mana into.

I wouldn't use that many 1 and 2 offs. Splitting key-cards, like [[Infinite Obliteration]]/ [[Memoricide]] is OK if you fear [[Extirpate]]/ [[Surgical Extraction]], but otherwise I would focus using cards 4 times to make sure you draw them when you need them. Another way of making a high number of 1-offs playable would be tutors or massive carddraw.
The problem with high-mana cards like [[Hex]] or [[Sorin's Vengeance]] (The classic sample for blue would be [[Traumatize]]) is that the time you can play them, they they often aren't that effective any more. You have a high number of removal in this deck, so the time you could play [[Hex]]...you opponent won't have enough creatures to make it an effective spell. [[Sorin's Vengeance]] simply might be an overkill at that time. Yes, [[Crypt Ghast]] can double you available mana, but again, it's a 1-off and it also need 4 mana. Which brings me to the next point: Access mana generated by [[Crypt Ghast]] cannot be used effectively as you don't have anything to sink access mana into.

The questions I'm asking when building a deck are as follows: How do I want to win? What do in need for this? How often do I want to draw a certain type of card (removal for example)? What are the enemy I will be weak against? How often do I encounter those? Do I need some cards that are very effective against one of those decks (but less effective against others) in my mainboard?
I'm trying to answer those like I would, when building this type of deck (Based on my experience, with modern generally and especially pauper mono black control)
How do I want to win: Control my opponent and don't let him do what he had in mind. Can be done by removing creatures he controls or cards from his hand.
What do I need for this: Point-removal, carddraw so that i don't run out of option, some (few) mass-removal, some discard spells to see what I'm up against, creatures that can break through my opponents remaining defense or alternate wincons
What are the enemy I will be weak against: Decks that have creatures that are hard to remove (Boggles), decks that don't have any creatures at all (mill, burn) or token decks.
How often do I encounter those: Depends on your kitchen table. Tokens, Burn and boggles can be quite common enemy's. Mill is normally not that wide-spread.
Do I need some cards that are very effective against one of those is OK, but i wouldn't run 4 of those mainboard. e decks (but less effective against others) in my mainboard: Having something against boggles, like [[Geth's Verdict]] and against and against token strategys, like [[Bile Blight]] is OK, against burn and mill you would have to do a total strategy swawp, which is hard, even with the mainboard.

Some general card-suggestions that come to my mind when thinking about mono black control:
[[Gray Merchant of Asphodel]]... Very effective in longer games, where you can get some cards out that increase your devotion
[[Gurmag Angler]]... "only" a 5/5 but can make effectively turn your graveyard into a mana-source.
[[Sign in Blood]], [[Read the Bones]], [[Altar's Reap]], [[Viscera Seer]]... carddraw/ card advantage.
[[Defile]], [[Cast Down]], [[Go for the Throat]], [[Tragic Slip]], [[Bone Splinters]], [[Dismember]]... removal.
[[Eternal Thirst]], [[Blade of the Bloodchief]]... great in combination with removal.
[[Duress]], [[Thoughtseize]]... discard-spell. Has the advantage that you can remove a card and look at your opponents hand.
[[Evil Presence]]... can disturb your opponents mana-base.

[[Oona's Prowler]] is a rare, and I have limited the number of rare cards in this deck to 1(x4) and allready have used [[Varolz, the Scar-Striped]]. [[Faerie Macabre]] could be an option, tough I was looking more for a cc1-2 creature :)

Infect-decks normally try to be as fast as possible, as they only have to deal half the damage to win a game, so [[Forced Adaptation]] and [[Forced Adaptation]] don't really fit into this strategy for me. Another question is, if you can save mana to play your counterspells, as you normally want to play a creature or a spell each turn. [[Dispel]] is OK as it only costs 1 mana and can be used to protect your creatures or hinder your opponent a little bit.
Personally I would also swap out [[Cystbearer]] for 2 additional [[Evolution Sage]] and throw in some searchlands, like [[Evolving Wilds]]. If you want another cheap infect creature then [[Ichorclaw Myr]] could be an idea.
[[Artful Dodge]] and [[Ghostform]] might be a little bit to much evasion as you have to remember that you have an opponent, which will likely deal with some of your creatures. [[Evolution Charm]] could be a versatile replacement for this. [[Rancor]] and [[Groundswell]] would be other cards that are normally used in infect decks.
Last, even if the deck is only played at the kitchen-table I would swap out [[Counterspell]] to get a modern legality. Because someday you might want to play at a local tournament and can't...because of 1 card.

bang, bang, bang, please add a description, because some of your card-choices are...interesting...for an infect deck, that normally tries to be as fast as possible.

A deck-description would be a good addition (for all of your decks), this helps us to help you. If you don't know what to write, I have tried to collect some ideas in an article deck (https://www.mtgvault.com/muktol/decks/why-you-should-add-description/)

[[Hangarback Walker]] could be an idea. gets you something to block early on, and if you have [[Anointed Procession]] on the battlefield, you get double the number of Thopters when it dies later on.
Against burn, discard or mill I would rather use [[Leyline of Sanctity]]

+1
Maybe [[Tempered Steel]] instead of 1-2 [[Intangible Virtue]]?
The deck looks relative slow tough, so what is your plan on staying alive against aggressive decks?

+1
Actually [[Blighted Agent]] is a pretty bad choice for a ninja deck in my opinion and this has a very simple reason: Infect. If you want to use him to bring your ninjas with ninjustu into play, he won't deal damage, and if you use him to deal damage to your opponent, you add a second type of damage, that doesn't fit into your game-plan. If you deal 9 damage with [[Blighted Agent]] and you opponent manages to get rid of him (which is pretty easy as he doesn't have hexproof) you have to wait for another one to finish the game with infect or deal 20 additional, "normal", damage with your ninjas.

Some suggestions from my own ninja deck:
[[Ornithopter]], [[Signal Pest]], [[Familiar's Ruse]], [[Ronin Warclub]]

Even more creatures, when [[Starnheim Aspirant]] is on the field. Would need some tests to determine if a playset would fit into the deck.
There are several forms of budget, the question is, what is your/ or you playgroups (from what I read in the upper post) approach to "budget"? :)
I would make a 2/2 split between [[Fiend Hunter]] and [[Oblivion Ring]] as the ring is very versatile and can hit creatures,
enchantments and artifacts, while the hunter "only" can hit creatures. [[Bonds of Faith]] could also be an option and is also versatile.
Another option would be to go for carddraw ([[Bygone Bishop]]) or revival ([[Order of Whiteclay]])

+1
Personally I would remove [[Soul Warden]] because you don't play enough small creatures (in comparison to a token deck). [[Answered Prayers]] could also be removed because it doesn't help you with enter the battlefield triggers, as it's already on the battlefield and simply changes from enchantment to creature.

Some suggestions, to replace those cards:
[[Answered Prayers]] should work like a charm with [[Bishop of Wings]]), [[Luminarch Ascension]] (Can take care of excess mana), [[Seraph Sanctuary]], [[Shalai, Voice of Plenty]], [[Serra Avenger]], [[Lyra Dawnbringer]], [[Angel of Jubilation]]
Personally I would also include something like [[Oblivion Ring]] to be able to interact with threats your opponents puts on the field.

[[Cranial Plating]]?

I know that this criticism is true for most of my decks and I fully understand it, but it's simply fun to build them and I can spare the time. As I'm no competitive player, never was and never will be, I don't know all the archetypes that are out there. Some I know of, others I stumble upon, take the idea and transform it to my likings (For example Boros bounce was transformed into mono white bounce) others are completely new to me.

When playtesting the decks I often see how... weak... the concept is. When building these things I have a tunnel-vision, but afterwards one can only slap his head and say "Why didn't you think of that". At the moment I'm thinking to either delete decks that behave horribly in tests (like this one) or to keep but unlist them.