One thing I really notice is how obvious the make-up can be. I like the episode "11001001" but the headpieces for the Binars really stood out to my eyes. The colour change from their faces to the scalp didn't look gradual enough. And In "Too Short A Season" Jameson's old age makeup looks even worse than before.
You should check out the shots of the dying Klingon in "Heart Of Glory". When they are shooting up his nose you can see where his real nose ends and the fake Klingon one begins, and all the prosthetic glue that was used.