1. Anya Jenkins (BtVS) - I'm always kind of surprised that Anya wasn't more popular given that she was kind of a mesh of Cordy and Spike who were both very popular characters. I guess I have a bit of a thing for otherworldly characters trying to intergrate with and understand humanity (hello Castiel)
2. Lilah Morgan (AtS) - I really wish we'd seen more Wes/Lilah in the show because I found them fascinating as a couple and her a really interesting character. I mean she started off as a fairly two dimensional villain (especially when standing next to Lindsey) but she really grew as a character when we started to see some of her fears and doubts while she was in competition with Lindsey
3. Gaius (Merlin) - There's so many fics out there that deal with Arthur's relationship with Uther but so few that deal with Merlin's relationship with Gaius and I do think he gets overlooked because Richard Wilson isn't as attractive as Anthony Head. I love Gaius, and I love the episodes that deal with his past and the role he had to play in The Great Purge.
4. Martha Kent (Smallville) - I really think the show suffered a loss when Martha left. I know it was necessary for Clark to grow as a character but she provided so much needed support to all the characters in the show. She never really had much of a storyline herself but I really felt the loss when she left
5. Bela Talbot (Supernatural) - Yeah, yeah, throw things at me now. What? I liked Bela! Eventually. Seriously, on a second viewing I found her to be kind of awesome. I mean she's clearly one of those characters you love to hate (like Zachariah) but the love is still there. It's just a shame her storyline had to get hacked because of the writer's strike