Still out of the loop and thanks to everyone who's been able to answer my questions. There's a guy who runs Nimrod and Brainiac with Nova Blast on each of them as well as I think Fortitude and somethign else along with 3 really cheap TK pieces. I'm trying to figure out ways to counter this since I have not played it yet and heard its fairly devastating.

First question: On the first turn can a running shot Pulse Wave still damage your figures? Or are they safe so long as they're still in the starting area?

Second question: Can a Pulse Wave go through a barrier?

Third Question: If an opposing figure has Pulse Wave with a Nova Blast attached to it that has no been used, is it possible to Mind Control that piece and have it use its Nova Blast on a running shot attack?

1) You always have first turn immunity, provided your characters are still in their starting squares....they can move out and back however and still keep it. I'm not sure how this works for characters that can start outside of the main starting area (because of a BFC)

2) No. Barrier is blocking terrain. There have been crazier rulings...but just like PW doesn't "deactivate" super strength (forcing the dropping of objects) I don't think a PW would "deactivate" barrier (assuming that a LoF exists between the PW-er and the Barrier-caster)
-Check the FAQ for more info

3) An opposing teams feats cannot be used during a Mind Control-ed action...so Nova Blast is right-out.

Awesome thanks!

What happens when some of the figures move out of the starting area and others don't, and I take a running shot PW into the thick of it? Can I make the Pulse Wave at all, damaging only the unprotected figures, or am I forbidden from taking the action as it would normally affect immune characters?

You cannot damage the figures that are protected by first turn immunity. Period.
Anyone who has already moved is fair game to be attacked, and will therefore be damaged.
Also, note that Pulse Wave does not require a target to use - in other words, if you want to do a Pulse Wave (or even a Nova Blast) without a single other figure in range, you are allowed to do so. It might not be the smartest thing in the world, but it's allowed.

One thing thing here might be a little paradoxal though. Say a figure does a standard Pulse Wave with 2 other figures in range, one being protected by First turn Immunity and the other not. Would the unprotected figure take full PW damage or just one click, since there actually is another figure in range? I think so, but I'm not sure...

What about Infiltration'd characters, who've used the BFC to start outside the starting area? Do they still get the first turn immunity or not?

Thats the BFC I wasn't sure of...personally, I think the first turn immunity rules are slightly botched: A figure that takes an action in the first turn (even a free action) should IMO be fair game for a retaliation.

I'm hoping Pulse Wave gets a slight touch-up...I like that it counters so many uber-defense tactics (Mystics, Stealth, Shared Defense, Sidekick, etc. etc.) but I'd really hate to see the game just turn into rock-paper-scissors.

Infiltration's a feat actually. I'm actually considering playing that with Taunt on a Vet Hand Ninja with BCF as cheap bait to keep my core units from getting a nova bomb right away.

No... Infiltration is a Battle Field Condition... it has a purple top...


Anyways, I have a small question too:

Can I use my Nova Blast with say Unique Doctor Doom and Novablast on an inside map, targeting walls as well?

Pulse Wave does not work on walls or objects.