Oh, this is a toughie. I'll do a top five.
1) Samajima Mamimi(FLCL) has a certain infectiously sweet air about her that simply puts you into a good mood. Sure, she's a little messed up in the head and started
doing...bad things to poor Ta-kun, but you've simply gotta love her!
2) Reidman Yomiko(Read or Die) is such an unsung hero that I simply have to single her out. She's not at all what you'd think of when you think of an anime hero, and she has the best super power ever. Who'da thought that paper could pack such a punch?
3) Aoyama Motoko(Love Hina) started out as a stupid man-hating-super-strong-swordswoman steryotype, but by the end of the manga or the anime she was a vibrant, but very insecure young woman. The character development involved was simply fantastic.
4) Ichihara Yuko(XXXHoLiC) is the singluar most misterious and sensual anime character I've ever seen. Sure, she's a bit of a wack job and sure, XXXHoLiC isn't an anime yet, but that doesn't even put a dent in her awesome...ness.
5) Faye Valentine(Cowboy Bebop) Three reasons:
1. Just LOOK at her.
2. She's not your average femme fatale, she falters on the job.
3. She's got a nice backstory.
Yeah, no guys, I know. Hope you're not too disappointed that I'm not making you drool over countless bishounen ;)