1. For Emrakul, I think Diabolic Edict is better. You need to answer him ASAP, if they get one swing in it's pretty much GG. And with Show and Tell he's likely coming down earlier than turn 4.
2. For Progenitus, Perish is better because you'll hit everything in RUG/Bant.
3. [edit: NVM you are correct, it can copy the artifact and give you a germ.]
Given how the new metagame is shaping up, I think there are a few sideboard cards that need to be strongly considered:
-Null Rod answers Painter Stone effectively, as well as completely hosing MUD and Affinity and other random artifact-based decks. It also has utility against any deck using Stone Forge Mystic. I would run 2-3 at your next tournament if you suspect you would see any of these decks.
-Graveyard Hate, in the form of Crypt, Relic, Spellbomb, Extirpate, or Surgical Extraction is pretty much a necessity if you expect to see Dredge or the combo decks relying on graveyard interaction (Cephalid Breakfast, Pattern of Rebirth/Hulk). I would run at the minimum 3 pieces. There was a period of time when GY hate wasn't really essential for this deck, but with the upswing of blue control decks, I'd expect to see more people opting to play Dredge and possibly other GY strategies.
-Lategame bombs such as Sower of Temptation or Consuming Vapors will make aggro matchups a bit easier to handle in addition to more standard cheap removal. Ideally you want to set up a situation where you've staved off the first wave, have a Goyf to block and a Stalker to attack. Then with your bombs you can turn a losing board position around.
-Mass removal dependent on your metagame. I've been loving Pernicious Deed because it has so much utility, but if you expect a ton of Merfolk Llawan is a great choice, and against the RUG/Bant/Zoo decks, Perish is better. 2 Slots minimum.

