Some of the most interesting aliens to me are ones that were treated pretty much as throw-aways.
The Forest seen in The End of the World -- I don't see the idea of plant people explored in Sci-Fi that often. Mostly just in fantasy. The thought that the species is descended from the trees of Earth is quite improbable, but very Doctor Who-ish. I wish we could have seen them again.
The Fish-people seen in the Doctor's daughter -- I guess originally these people were given actual lines that were replaced with bubbling noises. If they could make a translator for them then it would be great fun to see them again.
These species had the ability to produce individuals that were --well, individuals, and not just swarms of monsters. But I think their design indicates that they would have some interesting views on the universe than most of the bipedal mammal aliens and near-humans.
Actually, my favorite Dalek story in Nu-Who was "The Daleks in Manhatten." The Daleks recognized that in order to keep exterminating the universe they were going to need to change, and so they tried to create a new breed of Dalek -- but then couldn't accept change when they came across it.
I do enjoy the Doctor Who staples, though. They're always good fun, so long as the writers keep thinking up fresh ways to use them.