I had hoped somehow House was Omega, still hiding outside the universe.
I kept hoping that Omega would turn out to be the one behind all of that stuff with the Silence. He would have the necessary knowledge for how to blow up the TARDIS and has a well documented grudge against the material universe. Oh well...
Since we're talking about Who EU monsters as well, how about the Chelonians, one of the main villains of the New Adventures (Well at least the ones written by Gareth Roberts)?
http://tardis.wikia.com/wiki/Chelonian
I dunno. I read "The Highest Science" and didn't really care for it. The kind of came across as Sontarans if the Sontarans laid eggs.
What about the Ogrons? No one has mentioned the Ogrons yet. I just love how profoundly stupid they are.
Sil might be fun.
I vote for a return of the Rani, ideally played by Claudia Black.
And I think it's shocking just how rarely the Draconians ever appeared on the classic series. They seemed very well developed in "Frontier in Space" and they looked fantastic!
Ooh, The Ogrons, yea cool, they could be updated excellently (And we've already seen them in the last few years posting in TNZ

)
Claudia Black as The Rani...Hmmm...I think I'd really like to see how that turned out. I could imagine a cross between Aeryn Sun
and Vala would make a most awesome Rani

I also think Vala's Daughter Inara, played by Morena Baccaran could do The Rani justice (I loved her protrayal of Anna in NuV Series [one of the only awesome things NuV had going for it

])
I've already spoken up for the Draconians. I love (And treat as Canon)
Mind War unofficial Spinoff(s) because it's more Draconian Footage. Draconians are definitely on the top of my List.
The Master, yes, but, I don't want to see the same goofy portrayal it became (Though after a couple rewatches, there was quite a bit of Simms' Scenes that weren't Goofy, there were just a few scenes that tarnished his whole portrayal in memory on that first rewatch). So, if Simm (and/or Moffat) wanted to try Simm again, making sure to avoid Goofy, I'd be up for his return, but, I'd also definitely be into a recast more in the James Bond Suave, but, evil and devious while being Car Salesman Slick, kinda way Delgado did it. If we could go old enough, I've also always had a fantasy of Alan Rickman playing The Master, so, now's the time to do it, if I can still have my dream
Omega, yea, could be cool (Probably make a lot of Internet Heads explode if it was only a one off episode, and not the Season Long Arc, that's been predicted just about every NuWho Season/Series so far

)