So... I went through Shadowmoor and Eventide again, picking out interesting colour/counter play cards. I am not sure on all of these, but 'ere we go! (Sorry for there being lots here, but I want to use this post for my reference later as well.)
Hatchling Cycle:
As 4 mana 6/6s go, these seem pretty bad. I can't really think of any sort of deck that wants a card like this, they are a bit too slow for aggressive decks, and I am sure midrange can do better. They do cross over well between multicolour matters and counters though, which is why I listed them.
Colour-matters Aggro cards:
With the push I am trying to give multi-colour aggro, these cards seem pretty decent. Mudbrawler Cohort is pretty dependent upon 1 drops, but stuffing Red full of 1CMC creatures is Cube 101 (not that we shouldn't question that, etc).
Burning-Tree Emissary into Talara's Battalion seems pretty sweet, and I am sure with the density of hybrid 1 CMC cards, Talara's Battalion should be good. Are there any more of these?
Ballynock Cohort at 3CMC seems eh...
Ramp:
These two cards are pretty different, and curiously ramp better with either counter manipulation or colours... Should I double up on both?
Generic -1/-1 cards:
This section is pretty big, and of some pretty variable quality. Quillspike seems like it could be awesome in a deck that is heavy on persist, and some of the other cards seem really good in decks with proliferate to help kill creatures. Other cards just have counters so that you have something to manipulate. I think the most interesting creature is probably
Grief Tyrant. Removing counters from it makes it terrifying, adding counters transforms it into a kill spell, and as a bonus, it is a hybrid. That said, I think I would like to errata it to '...for each -1/-1 counter on Grief Tyrant, choose a creature and put a -1/-1 counter on it'. That way adding counters to it becomes an assemble your own
Plague Wind.
I am not sure about
Puncture Blast. It is a fine card, but I am still not sure about the strength of removal required for this cube. It may work out to being too weak, and that is ok, but I need to gauge the speed of the cube first.
I fear
Necroskitter becoming the centre-piece of a very terrifying deck,
Blowfly Infestation is similar. These two might be a little poison-principle, then again, I could simply think of them as good anchor cards.
Morselhoarder might cost too much. I am not sure how expensive ramp targets are going to be, but Morselhoarder into
Regal Force seems pretty sweet.
Scarscale Ritual exists. I have seen worse draw twos...
Other cards are variable,
Wickerbough Elder is almost certainly being included, where
Rendclaw Trow only makes the list because it has two keywords which reference -1/-1 counters.
Bloodied Ghost has the right hybrid mana symbols to match two sub-themes I am considering, and could be a 23rd card as a Wind Drake.
Persist:
I know there are a lot more cards than this with persist, but these seem the most interesting without being stupidly oppressive with heaps of ways to remove counters. Alright, that is a lie. Infinite
Redcaps could get old fast.
Safehold Elite seems like an easy to cast bear that turns on Shard-blades, while also being resilient and doing counter things. Yey! Cross pollination!
Furystoke Giant seems like a very interesting card, but as to how good it is, I don't know.
Restless Apparition seems pretty bad. I suspect it would be a more interesting card if instead of giving itself +3/+3, it put +1/+1 counters on itself... That is a bold bit of design that might be a little too courageous for Wizards though.
Sneaky Counter/Colour Stuff:
Come on guys, you knew
Gilder Bairn was coming...
Leech bonder and
Razorfin Abolisher work perfectly for how I envisage Blue. Manipulative, though as I am not sure either will be decent if spot removal is strong.
Swirling Spriggan. Redundancy! Yey!
Generic Hybrid stuffs:
Some of these are here so I don't forget they exist, others because I would like an opinion.
Crackleburr? - What does this do? Does it do anything?
Elvish Hexhunter? - I like my artifact/enchantment hate to have legs, and being a hybrid one drop is not the worst place to be in this cube.
Desecrator Hag? Seems expensive, but if I am planning to support Black devotion, does that change opinions?
Puresight Merrow? Genuine question-mark next to this one...
Tattermunge Witch? Seems a passable 2-drop that helps push damage later, not sure how gummy the ground will get yet though.
Valleymaker? Yeah... this is a card.
tl;dr; Shadowmoor block was pretty damn awesome.