Are there any classes that resemble an occultist of the Lovecraftian mythos, or have such a feeling, except the alienist and the flesh warper? The aberration blood feats are interesting but just give flavor; I am searching for something more solid, a base or prestige class.
The Lovecraftian feel is broader then most people think: You could easily have NPCs with the Dread Pirate PrC involved in your version of The Shadow Over Innsmouth. I also based this on what I could see appearing in Lovecraft's stories, rather then just Mythos type creatures (Thus degenerate humans and such are also fair game, as are charismatic cult leader types, etc). Howard, a good friend of Lovecraft's, also published stories in the same vein, but a bit more hack and slash. I've denoted classes that would work well with his books.
The other idea is to take rules from a class, then rewrite the theme and feeling of it to be more lovecraftian: Example: Bear Warrior instead is embracing his Shoggoth heritage, and becomes more and more unnatural as he goes up in levels.
However here are some which I could think would be useful or lend themselves to Lovecraftian work:
Complete Adventurer: - Animal Lord (Sharklord, Apelord [Degenerate humans]) - Master of Many Forms (Change into Ooze and Abberations) - Ghostfaced Killer (More Howardian horror, but it goes well with Lovecraftian horror)
Drow of the Underdark (Based only on names)
Heroes of Horror (names again), most of them
Libris Mortis: Pretty much all of them
Lords of Madness: Pretty much all of them
Magic of Incarnum: All of the ones that involve merging Incarum into yourself.
Tome of Magic: All of them, binding dead shades to serve you. Particularly the binder.
Eberron Campaign Setting - Master Inquisitive (for investigators)
Races of Eberron
Champions of Ruin
Player's Guide to Faerûn
Serpent Kingdoms: Pretty much all of them
Of course, the Alienist class from Complete Arcane is specifically designed to be Lovecraftian in nature. They summon pseudonatural creatures. The D&D 3.5e version isn't OGL but here's a Pathfinder conversion that gets the general idea across. There are similar ideas in Gates of Firestorm Peak and the 3.0 Manual of the Planes, and the 2.0 Illithiad.
I'm also currently at a loss for classes that are directly inspired, but there are some things that could work well with a little reflavoring.
I don't think there are any others to be honest. The closest you will get is the Lords of Madness supplemental book.