So, tossing aside overlooked or neglected, some of my favorites:
Impure Blood A not entirely human gladiator gets a chance at escape, and finds him in the midst of many intrigues.
Endstone A Sword&Sorcery adventure in a very weird United States. When it says something weird -- like, our obviously human-form heroine is a deer -- you are getting a clue about the world. And how many stories make you wonder whether the guy trying to destroy the world is wrong to do so?
Rusty & Co. The D&D adventures of a group consisting of -- well, a mimic, a gelatinous cub, and a rust monster. Funny.
Bird Boy A clumsy young boy stumbles into legend. (The prologue is a little different from the rest of the tale.)
Gunnerkrigg Court A strange school: "Within the first week of my attendance, I began noticing a number of strange occurrences. The most prevalent of these oddities being the fact that I seemed to have obtained a second shadow."
Thistil Mistil Kistil Posthumous adventures among the Norse gods.
No Rest for the Wicked a world where all the fairy tales are grimly true. Even if it's very slow in updating at the moment. (Like, once in the last year.)
Tales of the Questor In which a talking raccoon wants to be a hero in a fantasy world. Not quite as good but still fun Quentyn Quinn Space Ranger a tale of his descendant-- and I think it's found its grip after some initial floundering.
Sandra and Woo A girl and her talking raccoon. Not like the last two, which were anthropomorphic animals.
Order of the Stick Stories in a D&D world -- very funny, but you have to give it a chance to get going past the gag-a-day to get to the plotlines. (It also gets better for non-D&D fans then. And it's quite good.)
Girl Genius In which mad scientist rule the world -- badly.
Derelict Scavenging in a post-apocalyptic world.
Wooden Rose A Victorian tale featuring two sisters living by an enchanted woods, and the mysterious stranger who meets them.
Roza the Cursed Mage A girl trying to undo a curse
Erfworld Life in a turn-based wargame! (Yes, it does some silly spelling stuff. Overlook that.)
What are some of your favorites that you want to recommend?
Part of bittercon .