Samuel L. Jackson's character in Die Hard with a Vengeance. Seriously wrecked what was already a relatively unimaginative sequel. His constant racism is so irritating, it's probably the single most influential factor that causes me to skip #3 and go straight to #4 anytime I watch the series.

With the Star Wars prequels, there are almost too many characters to count! Jar-Jar, lil' Ani, older Ani, Padme, Jango, Boba, Sidious, Grevious, Yoda...really the only enjoyable characters IMO were Qui-Gon (whose impressiveness seriously dissipates when you start analyzing his actions), Obi-Wan (who didn't totally suck and had some memorable scenes, but oftentimes comes off as bland) and Palpy in ep. 1-2 (but his absurd self-parodying performance in ep. 3 basically cancels out his earlier respectable portrayals entirely). Of course, the problems with these films transcend bad characterization...poor writing and direction is probably more of a train-wrecker than the bad characters.

Aaaaand, to depart briefly from the negativity, I'll cite Captain Sheridan in Babylon 5 as a character who really helped the franchise. While there was nothing really terribly bad per se about Commander Sinclair, he just wasn't as inspiring a character as Sheridan. To be honest, I've always felt like season 1 is really just an extended introduction to the real series, which begins with season 2.