Gee. You left ALL the cool ones off the list.
I think Drow are Ok, but WAAAAYYY overdone, and more often than not - done badly (see RA Salvatore).
Duegrar and Sverfneblin (and heck the Drow themselves) are part of the way overused concept of 'The Things in the Underdark are a Whole Lot Cooler than their surface counterparts'. The minute you play that card with me, I go looking elsewhere. And you can pretty much judge the quality of a roleplayer as inversely proportional to the number of times he's played character's of one of those three races.
Koa-Toa are another creation of G.G.'s where it is clear he is going, 'I so need a NPC race that can challenge the characters because my game system so clearly falls apart at higher levels'. Since that is no longer the case, I see no reason for KT to come back.
Beholders are pretty cool, but I don't like presenting characters with that many oppurtunities to die just because of a bad roll so I don't use them.
The coolest Underdark races:
Trogoldytes ought to be, by thier very name, the standard deep dwellers in any campaign. They have fun abilities and attacks without being 'I'm so overpoweringly tough its clear my designer was trying to impress you with how tough his monsters are'. Of course, they were horribly broken in 3 ed. until the errata.
Goblinoids (Goblins/Hobgoblins/Bugbears) are good challenges anywhere and everywhere and seem to provide a richer oppurtunity for a unique culture than the overused and over trite Orcs. They also can be good 'neutral reaction' races if you want your PC's to talk to something. For one thing, PC's are likely to know the language. For another, the PC's know that the treasure that the Goblins have isn't worth thier time, so maybe the information might be more useful.
As a DM, how can you not have a warm place in your heart for Kobolds?
Stone Giants can be fun if you need a good awe inspiring underdark culture that isn't a) immediately lethal and b) trite.
Cloakers are awesome, with a wide variety of powers, very alien, not ego driving, not likely to become a PC powergamer race, and are capable of challenging players of almost any level depending on how you place and run them.
Ditto the Aboleth, only more 'run in terror' and less suited to challenging mid level characters.
Ditto for Mindflayers, although the mechanics of Psionics have always been and still or problematic.
But the award for the most neglected (and cool) Underdark race goes to...
DARK CREEPERS and DARK STALKERS!!! The most atmospheric and interesting of the deep races. Humanoid but utterly alien. Powerful but with clear (balancing) weaknesses. Weak enough to present to low level characters. Potent enough to challenge anyone if you feel inclined (Dark Stalker Shadow Dancer's anyone?)
