Here's a big ol' list of questions that I though up in the space of an hour. Some of these questions I already know the answer to, but I think they're a good idea to have in a FAQ.
If Wild Sorcerer or Wild Reincarnator is played in a multi-power game, how many powers are affected and who chooses which ones (if not randomly)?
If Healer heals someone, are their ships removed from the Warp or stopped from going to the Warp? (Asked because, if ships are sent to the Warp and then healed, Remora could cling and get ships every time Healer heals.)
Can Healer act before Zombie evades going to the Warp?
Is there an official ruling on Zombie vs. Void other than the standard timing rules?
If ships are sent to the Warp during Reveal, does Warpish update his total accordingly? (My guess is yes.)
Why does Gambler say "Do not use with Sorcerer"?
Can Vacuum use its power on itself, and if so, can it cause an infinite loop?
If you attempt to play a Flare but it gets Card Zapped (or for some other reason it is stopped from being used), does that count against a player's limit of one Flare per encounter?
Can a player use Wild Amoeba to increase his ship count if he has no ships as the defense?
Can Will attack Blue on Red's planet even if Blue has no colony there? (I'd say no, but the text doesn't specifically say.)
Can you research and reveal a Tech at the same time? (So, if the Tech needs 2 ships, could you place the 2nd ship on the Tech and reveal it in the same Regroup phase?)
If Warrior gets zapped, does he still earn experience? (He doesn't need to use his power to earn experience, but once he's zapped, he loses his power for the rest of the turn.)
If you get Force Fielded, are you then affected by Grudge?
If you must lose ships that aren't in the current encounter (such as Grudge), what happens if you have no ships outside the encounter?
If you have no ships outside the encounter, can you still invoke effects that require sacrificing a ship from outside the encounter (such as Wild Void) by sacrificing one that's in it?
Can Fido pick from any encounter cards discarded in the encounter (such as those lost by the Plague), or must he pick from the ones that were actually played?
Does Human's zap-him-to-win beat Pacifist's play-an-N-to-win? (I would rule yes.)
If the Omega Missile destroys a planet, do you still need three home colonies to retain your power?
If Warrior draws his own colour and reclaims an empty home planet, does he collect experience?
Does Hate have to be zapped before he chooses which card to discard?
If Super Amoeba oozes all of his ships out of an encounter as an ally, is he considered to have allied in the first place (for effects such as Grudge and Wild Mutant)?
Why must Spiff's total be "10 or more less", instead of using his power when he "loses by 10 or more"?
If Pacifist must play an N when Loser calls upset, does he get compensation? (I would say yes.)
If a power such as Calculator, Mirror, or Tripler affects a card, does an M copy the card's value before or after the modification? If the power is used in Reveal and gets zapped, does the M take on the card's original value?
If an encounter card is altered by something other than a power (such as Wild Pacifist), does an M copy the alteration?
Does the defense choose which ships die to Gluon Mines? Can allies be removed from an encounter completely because of them, and are they considered to have allied in the first place? (As Super Amoeba above.)
If Sorcerer switches cards, which card does Clone or Filch take?
Can Filch take Gambler's unrevealed card, and if so, can he notify the table whether the truth was told?
If a Flare that can be played at any time changes hands, can it be used a second time in the encounter by the new owner?
If Vulch gets zapped, does he get the Zap that zapped him? (I would say no, since he loses his power for the rest of the encounter.)
Does an M count as an attack card if it duplicated an attack card? (For the purposes of Cudgel, for example.)