The permanent one: I'd say Angela Petrelli, but as far as we know, she isn't a Hero, as we don't know for certain what her power is (if any, same with every other member of 12 except for Linderman, Parkman, Bob, and perhaps Devoux) - Mohinder and HRG fall into this category too. We can rule out Micah and Molly as I doubt that NBC would kill kids on a show like this (although they do it on SVU so???). My guess is Bob gets wacked by Elle with the lightning in the Primatech Basement. - It also fits the "get rid of the original 12" theme and the distrust that is being cultivated between her and Bob. My guess is she learns that he isn't her real Dad, gets pissed because of the way she was treated for all those years, and because she is a psychopath anyway - cooks him. If this ends up being the case - who ends up controlling the company, and can the company be turned into a group of Heroes (Parkman, HRG, Mohinder, Nathan, etc.) that will end up fighting the virus?
The uncertain one: Hiro either by Adam/Kensi or Peter protecting Adam. I think that Adam is going to succeed in releasing the virus, which will setup the story line for the 3rd volume "Exodus". Either way wacking Hiro will provide the "*hit hitting the fan" feeling that the spoiler predicts. What is intriguing about Nathan being the uncertain one is that in the virus future didn't they say the virus was "air-borne"? Perhaps he gets stuck by Adam with the 128 strain and goes for a flight back to NY to visit Mohinder - perhaps this is how the virus gets spread, kinda far fetched, but that is what makes this a "Dark Horse" prediction.
The one who will be brought back: This is the toughest because it could be several people - I think it will be Sylar. I think he ends up with 1 of the vials of Anti-Virus and ends up injecting himself with it. The way he would "die" is more peculiar. My guess is he doesn't get his powers back until he injects himself with the vaccine, but either gets shot by Parkman or Mohinder - or through some other misshap, falls out of the window in Mohinders loft ending up in an alleyway. (This brings up the question I have had since Adam injected Nathan with his blood - We still don't know how Sylar acquires his abilities - could simply injecting himself with the vaccine be enough for him to obtain the regeneration ability, would it work the same with Nathan & HRG?) If not Sylar - then possibly Nikki for the reasons mentioned above (either via the virus or via trying to save Monica - and subsequently saved by the vial of vaccine). I would also say Adam/Kensi for obvious reasons (except that the spoiler seems to indicate that it will be via the use of Claires blood) - perhaps he gets wacked by Peter and Hiro after Peter learns the truth about him. This could also fit with my "Uncertain One" prediction too as he could release the virus after everyone thinks he is dead.

. DL, Season 1, getting shot almost dying, yet being able to be part of "Saving the World", then becoming so much more as in a true family man AND a true Hero as a fireman. Then tragically being gunned down and dying in a nonsensicle way.