There's really a little bit of everything out there. My notion of quality alters a tad at midnight, and these are the most obvious choices - I'm sure Pepper has more unique contributions!! :)
Some of these may just be open real late...
Steaks - Pacific Dining Car (downtown)
Delis - Canter's (Fairfax) & Izzy's (Santa Monica)
Italian - Damiano's (Fairfax)
Thai - Toi (Hollywood)
Coffee Shops - Pantry (downtown) & Swingers (Beverly & Santa Monica)
Mexican - La Cabana (Venice)
Eclectic - the standard (Sunset) & fred 62 (Los Feliz)
You seem to have nailed a lot of the good ones. You could add to the list Suehiro in Little Tokyo for Japanese greasy-spoon food and the Shibucho on Third near Hoover for sushi (not quite the same as Tom's beloved downtown Shibucho, but good nonetheless.) Most of Thai Hollywood is open until 4 or so: Kruang Tedd, Ruen Pair, Sanamluang, Torung. Happy Valley serves great HK-style seafood in Chinatown until 3. And Mayor Riordan's forgettable Pantry is open 24/7. I sure do miss Ship's, though.
I sometimes go to Sittons on Magnolia west of Lankershim in North Hollywood. It's not really that good, but it works, and there's a pretty interesting crowd - real "only in Hollywood" people, except they're also very East Valley too... There's sometimes a suburban metalhead vibe going on.
I used to keep a list of late night munching on my website, but it's been down for a couple years...