Can I point out the fact that the things you have listed are game publishers not developers? Therefore they should aquire none of them as it would waste alot of money. Business-wise, it would leave a gap in the market, which would just be filled and therefore even more competition which could mean less sales.

If were talking developers, Quantic Dream all the way.

From Software would be a great choice.

Microsoft and Nintendo is next.

What I'd love is for Sony to step in and save the developers at NIS and make some first party Disgaea and other JRPGs.  It wouldn't be the best move for Sony from a business aspect but it would make me so happy. I hate seeing NIS in such harsh times.

Realistically they should probably get That Game Company, Quantic Dream, or Q-Games.

Warner Bros.

I said that like 2 years ago. No one was happy to hear about the idea of NiS being tied to a major publisher citing that it would hurt their freedom. [Which i really don't think it would when I look at SONY projects like Heavy Rain and LBP]

If NIS was doing gang busters I would be inclined to agree that it would be preferrable for them to stay independent.  Sadly they aren't and I agree that being under Sony would probably not have much of an effect on the games NIS put out and if it's a choice between NIS under Sony and no NIS at all I would definitely hope for the former.

but as I said this is more of a wish than something I think could actually happen.

Nintendo or MGS

probably the most impact: EA (aside from MS and Nintendo)

most realistic: Qunatic Dream (to prevent future multiplats, David Cage already made  remakrs in that direction.)

Unneeded: Sucker Punch (They only made Sly Cooper series and inFamous series, which are already Sony exclusive.)

Revenge buy: Infinity Ward (for "betraying" Sony and going Multiplatform with EA)

Wasted money: Square-Enix (Even though Sony could lead Sqaure-Enix to new glory, their games aren't million sellers anymore. They would waste more money on the buy than they could recoup in 20 years.)

aquistion with the biggest fanboy impact: Bungie (I would LOVE to see that one :D )

and last: Wildc*rd: Gamefreak plus the Pokémon Company (Pokémon exclusive to Sony? Meltdown of the Universe :D )

From these five, only Atlus and Level-5 are somewhat plausible, but I still strongly doubt, that they'll "acquire" either of these companies.