Adipose - 1
Carrionites - 2
Clockwork Droid - 3
Gas Mask Zombie - 2
Gelth - 2
Judoon - 3
Peg Dolls - 1
Pyrovile - 1
Scarecrows - 2
Slitheen - 1
Sycorax - 3
Tritovore - 1
Vashta Nerada - 1
Some aliens in Doctor Who are simply designed for a single use, or rather the plot they serve makes them utterly unique. For instance, the very effectively scary gas mask zombies were a superb addition to Series 1. But their origins (the Nanogenes) would make it very farfetched for them to appear in that guise again. The Nanogenes themselves could serve a future story (in fact they did - Asylum of the Daleks) but the gas mask element was a one-hit wonder. Similarly I feel that the Peg Dolls, Adipose or the Vashta Nerada are aliens very limited by their capabilities, and would feel very repetitive if used again.
Some designs are simply clunky - the Slitheen, whilst it's possible to see what was envisioned are a cumbersome design that is best left behind. Others, like the Pyroviles, served their plot brilliantly but don't inspire much interest in a return appearance - especially when you only get a dozen or so episodes a year.
There are others you feel could warrant some kind of sequel to their original story if the right idea was in mind. The Carrionites are still screaming away in the Tardis presumably, and also aren't likely the only ones of their kind. Another story involing them could be intriguing if someone had a decent idea for them. The same goes for the Scarecrows/Jack Straws... they were given a relatively small role in their first story and were simply animated creations with no actual life of their own, which makes them a bit hard to bring back. But the idea of corporeal scarecrows would make for a great threat, and even if not quite the same as the ones seen before would be a great addition.
There are some alien species that are much more applicable to a wide range of stories. The Judoon, or indeed the Shadow Proclamation, could make a return appearance. I think the Ood could have another story in them at some point. The Sycorax are another who we hardly seem to know anything about, but who have shown up a few times in the background since their story. I think The Wire is deserving of a sequel (but then I quite liked The Idiot's Lantern unlike many) and one of the factfile books hinted at a second invasion attempt in the 1970's.
And one I'm sure we'll eventually get but haven't had in a long time is another Sontaran story. They've had just the one technically speaking since 2005, but there's plenty of scope for more.
Beyond that though, and the obligatory Daleks, Cybermen and Weeping Angels I think there should still be a fundamental focus on new designs - with Series 10 maybe aiming to deliver a new iconic threat, as it's been a while since we've had one.