In Hellsing, I feel like I'm one of the few people who likes Walter best when he's an elderly butler. It seems like the majority of Hellsing fans only like him after he's been turned into a vampire by Millennium or when he's a teenager fighting in Poland due to his more youthful appearance. But personally, I like him the most when he's elderly, because that's when he seems to be at his most serene, wise and gentle (except during the battle with the Valentine Brothers, that is). Kind of like the grandpa I wish I had.
In Trinity Blood, one of my top favorite characters is one that is almost always overlooked: William Walter Wordsworth, The Professor. I really like him because he's so jovial and intelligent; definitely someone I'd hang out with in real life.
In Gurren Lagann, I am really attached to Nia, even more so than the other main characters. I'm not sure how popular she is here in the West, but she must have some kind of fan-following in Japan to have so much merchandise based off of her (from figurines to pillowcases and even an artbook!).
I like Derek, Markus, Angie and Valerie from Trauma Center as well. They're overlooked characters, because even though the franchise is popular for its gaming aspects, the characters themselves don't seem to get a lot of fan-love.