Rem Savarem - Trigun
She's too good to be true. One of the few 100% positive anime characters I don't find annoying or dumb. I would have liked to pick Legato too... but he's not exactly "secondary"
Eiri Masami - Serial Experiments Lain
I'm not sure he's a strictly "secondary" character. Lain is like that, you can never be sure what you're talking about. This character is creepy, but very fascinating.
Panurus - Boogiepop Phantom
"All" of them. They share same weird philosophy about life. Which is kinda ironic, knowing what happens to both characters... The macabre irony of their case is irresistible.
Bunji Kugashira - Gungrave
Oh man, he reminds me too much of Kitano/Miike yakuza characters...
Straight Cougar - Scryed
He's the wild card of the series. Plus, he's a funny, genuinely cool and refreshing character. I could watch him appear and disappear all the time without being bored, even when all those fighting scenes in the series started to be annoying. The way he talks is great!
Ryoji Kaji - Neon Genesis Evangelion
Ah, this man... the man every girl wants to marry... no?
Menchi - Excel Saga
Is she a minor character? I don't know. Probably not, but depends on how you see things. As a food supply, I think she cannot be a main character. In any case, with her watery eyes she's too cute. Not as much as Puuchuus though...
Walter C. Dollneaz - Hellsing
As meryl said. I couldn't believe he was able to do all those fancy things at his age! Amazing!
Chiyo-chan's Father - Azumanga Daioh
The yellow neko-being with superpowers is amazingly surreal... Good girls must eat tomatoes or he'll get mad
Sumomo - Chobits
I want her! I want her! WANT!!! >.<
That's all I can think of for now.