Off the top of my head:
Some of the Best (Old Who)
-Sotek
-The "Robots of Death" (from the episode of the same name)
-The antagonist with the messed-up face from The Caves of Androzani (or maybe it's that the episode is just that good? I dunno)
Some of the Best (New Who)
-The entity from the episode "Midnight" (granted, it's more that the episode itself is excellent rather than the entity by itself being memorable)
-The Flood
-The Mummy
-The Sandmen
-House
-The Empty Child (or Empty People, since there's more than one of them by the end)
-The Vashta Narada (okay, they technically appeared in a pair of episodes, and also appeared in one of the adventure games, but as far as the TV series by itself goes, I think they can count as a sole appearance)
Some of the Worst (Old Who)
-The Dominators
-The Robot (from the episode "Robot" - bear in mind that the episode itself is decent)
-Those weird aliens in the episode "The Two Doctors" - y'know, the ones who just won't stop eating
Some of the Worst (New Who)
-The Reapers (in that while the episode they appear in is good, the Reapers as a concept make little sense - why only appear then, and not any other time the timeline's been botched?)
-That alien who imprisons children in the episode "Fear Her"
-The hooded guy in the episode "The Power of Three"
I'm sure there's more, and I'm probably selling a lot of them short by forgeting their names, but DW being as long-running as it is, that's a heck of a lot of episodes to trawl through). Truth be told, I think a lot of Doctor Who's best villains are reoccurring for a reason, even though some of them have had over-exposure IMO (e.g. the Weeping Angels, probably the daleks as well)