I'll be going through these in terms of mana cost as well. I consider all counterspells, removal, and board-wipes part of my board control suite. The goal of board control is to cement your board advantage or prevent a combo opponent from winning the game.
Annul - An important piece, since it prevents that Rest in Peace, Leyline of the Void, Torpor Orb, Grafdigger's Cage, Relic of Progenitus, or Nihil Spellbomb from ever hitting the board. It also handles artifact and enchantment creatures when necessary, and can take down combos.
Pyroblast / Red Elemental Blast - Nearly identical in function, their slight difference will almost never matter in a real game. Usually, there will be another blue player in multiplayer, and 1 drop counterspells/removal are too powerful to pass up. Redblasts handle a very diverse array of threats, such as counterspells, removal, Jace, combo pieces, and even blue commanders.
Swan Song - It's a swan! I love this spell in any format, and it's even better in EDH. Handling instants, sorceries, AND enchantments for one mana is a huge boon, whereas a lone 2/2 Swan token is a small price to pay, especially in multiplayer EDH with a stax engine. It's one of our best ways to handle enchantments.
Turn Aside - A wonderful piece of defensive magic, which shuts down opponents removal.
Rapid Hybridization - Hybridization is a 1 drop kill spell. A cheaper Pongify in a different tribe. As a fan of Pongify, I was so happy when this card was printed. It's even better in EDH, and like Swan Song the lizard is easily dealt with by the stax engine.
Vandalblast - A one drop shatter that turns into an asymmetrical wipe. Vandalblast the only removal in the deck that is limited explicitly to artifacts, but its ability to wipe the board, its low mana cost, and its cheap price make it well worth the slot.
Ertai's Meddling - I've gushed about Ertai's Meddling long enough. My favourite counterspell in the game, largely because it gets around spells that can't be countered. For 2 mana it wins counterspell wars, even against Counterflux, and it can counter Thrun. Keeping an opponent's win condition out of their hands for several turns is tantamount to removing it from the game entirely. Cast for 3 it gives players an interesting choice RE their commander - do they return the spell to their command zone, increasing its cost and forcing them to pay it again, or do they leave it in exile, hoping to get it for free in 2 turns? Spells that lose their last delay counter are cast as a copy of the spell in the state it hit the stack - this creates some interesting interactions with morph, and also gives you a second opportunity to counter the spell for real when it tries to resolve.
Memory Lapse - The dickhead's Remand. Put an opponent behind instead of coming ahead.
Into the Roil - Into the Roil may not be a hard answer to anything, but it's a soft answer to everything, and it can be kicked to cantrip. Worth keeping in the deck.
Negate - Since Black already has such great creature removal, I'm more worried about using blue to answer non-creature spells, and for two mana Negate does exactly that. Artifacts, enchantments, instants, sorceries... So long as it's not also a creature and can be countered Negate handles it.
Reality Shift - Exile target creature for 2, and at instant speed? Yes, please! Manifest is a weird mechanic, harkening back to Pongify. If a land or non-creature is exiled you've basically exiled a creature and kept an opponent's piece from them. If they lack recursion you've denied them the card entirely. Great creature removal, worth keeping in the deck.
Rakdos Charm - I like this card. I think most players do. Its key effect is artifact removal, but tacking on targeted graveyard hate and token hate makes it really valuable in any format it's allowed in, and EDH is no exception. Defeating graveyard strategies, handling artifacts, and killing anybody who manages to create a giant token army.
Sickening Dreams - Our first board wipe is also a combo enabler - drop your creatures into the graveyard and clear the field. A 2 drop wipe is a good thing to have, particularly one that's so flexible. You can handle a hoard of small tokens without hurting your own creatures, or go big and discard your hand to start fresh. It can kill walkers too, since it hits players.
Go for the Throat - Kill non-artifact creature. More splashable. Nnnnnnice.
Hero's Downfall - Strictly better Murder. Kills creatures and walkers at instant speed.
Ashes to Ashes - Exile two target creatures on one card for 3 mana? Saweeet! 5 life is a small price to pay for this. The real downside is you need two targets to cast it, but in multiplayer EDH that shouldn't be a problem.
Chaos Warp - Shuffle a permanent into an opponent's library. This is one of our best options to get rid of enchantments on the board in our colours. Shuffling a library ruins top-deck tutors. Its downside is more frustrating against decks with high permanent counts, so bear that in mind.
Crosis's Charm - For three mana, you get flexibility. Destroy an artifact, kill a creature, or bounce anything else, all at instant speed. It is a little expensive, and it can't kill black creatures, but I'd say it's worth it to destroy artifacts and creatures while retaining options against enchantments, planeswalkers, and indestructible things.
Nevinyrral's Disk - Black's OG boardwipe, and one of its best options against enchantments. I mean, it's technically an artifact, and opponents have a turn to destroy it, making it a little bit slow, but it's worth it for such a complete wipe. It kills everyone's rocks, however, so keep that in mind.
Kindred Dominance - You could use this spell to leave your Humans or Wizards intact. Or you could choose Dragons, to get a free swing in with Crosis. If you've used Necromantic Selection in turns prior and/or have the Nim Deathmantle you may choose Zombies on occasion. Or Praetors, to keep Sheoldred running. The deck lacks any tribal focus now, but asymmetrical boardwipes are useful enough for it to make the cut.
Necromantic Selection - You can steal on opponent's bomb with this, or merely protect your own important combo piece. All of the field wipes become more valuable with Marchesa, the Black Rose, but this one especially so. This field wipe also combos nicely with Flayer of the Hatebound or Puppeteer Clique.
Decree of Pain - You can cycle it for five, at instant speed and without using the stack, as a mini boardwipe that clears away 2 toughness creatures, including indestructible ones. Or cast it for 8 to wipe the slate and draw a tonne of cards. Either way, it's a useful piece.