Let's see how long this list is going to be.
From the '80s to early to mid '90's:
Spider-Man
Silver Surfer
Wolverine
Manhunter (the bounty hunter)
Sandman (golden-age)
The Hulk (John Byrne and then Peter David's run)
The Spectre
Storm (punk rock version)
The Flash
Supporting heroes (I know some of these characters had their own series at some point, but I liked them prior to that):
Silver Sable
Black Cat
Martian Manhunter
Big Barda
Currently, I don't collect many comics, so my choices are limited, but I'd have to go with Hawkgirl from JSA. And Martian Manhunter is still pretty cool.
As for all time favorites, I wouldn't trade my Spider-Man or Silver Surfer comics for the world, so they would probably be put at the top of my list. I'd also add the Grey Hulk during David's run and Big Barda of The New Gods (I consider her costume to be Kirby's best design ever).
I wouldn't trade my Claremont X-Men either. That series, however, was such an ensemble, all the characters were great for different reasons. Colossus, Kitty Pryde, Wolverine, Rogue, etc., were all great. There was more characterization in a team book than in most solo comics, sadly.
Punk rock Storm was pretty cool, though. I miss the '80s, when a 6 ft tall black woman with a white mohawk and dressed in leather could walk down the street and no one would bat an eye.
EDIT: How could I forget Doc Samson, the greatest crime fighting, green haired, jewish psychiatrist ever?!
![Big grin :D :D](data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7)