For U Doom, I'd have go to with Refinery (E2M3), mostly since it's kinda dull, and the intermission music feels out of place. However, it has some nice design and secrets. I don't hate it.
Doom II: again, I don't really dislike any map from this game, but if I had to choose one, I'd probably go with Tenements (Map17). Considering it was Romero, it does not at all follow his idiosyncrasies, and as such, the pacing and some of the enemy placement is pretty shitty.
As for TNT, there's about half the WAD I could choose from, but Administration Center (Map21) takes the cake. Massive, lifeless, boring, and normally empty, it's the epitome of the bad design that permeates this particular IWAD.
Plutonia, for me, only has a couple of bad levels, and I'd have to say the worst is The Final Frontier (Map24). It tries to be a more slaughter-oriented Living End, but I found the enemy placement to simply be obnoxious as opposed to well thought-out.
Master Levels for Doom II: I seriously can't decide between TEETH or Mephisto's Mausoleum; the former has extremely tight combat scenarios that may have seemed interesting on paper, but do not gell out at all in practice, and the latter has too many Revenants, and is stingy on the ammo.
NRFTL: I'd say Inferno of Blood (Map06) is the worst. Not only do the NRFTL mappers keep withholding the damn backpack (especially when this map in particular should really have warranted one), but the flow is kinda crappy, with some dumb enemy placement and an overlong secret hunt. Yeah, I know it's for a BFG, but still.
There you go, my picks for the official IWADs.