EVERYTHING seems to close in the peninsula at 10. It's horrible.

The only 24 hour place I've found is Heidi's Pies. Around the corner from me at 92 and El Camino. Not a great coffee place but it's open and it's got food.

Caffe Pergolesi, Jahva Man, and Caffe Espresso Royale (née Mimi Carpenters, right?) are great places. You really invoked some hardcore nostalgia; I graduated UCSC over 10 years ago... I never ran into anything as cool as those places during my 7 years in SJ (such is the magic of Santa Cruz).
However:
I enjoyed Mission Coffee on Campbell Avenue, in Campbell. The area's quite nice, and the vibe is pretty good.
Additionally there is a small coffeeshop in the Pruneyard Mall, which is right next to the newest Camera Theater (or *was* when I moved away 2 years ago). It's a little more socially aligned than Mission.

I agree that Pergolesi is great. And Cafe Royale has changed it's name, yet again, to Lulu Carpenter's, but is still cool.

I've always expected Palo Alto to have coffee hangouts, like other university towns I've been in. There is the Coffee House ("CoHo") on Stanford's campus in the student center, which has the hangout feel, does coffee, pizza, desserts, and beer until at least 10.

Outside of that, it becomes trendy restaurants (Il Fornaio, Zibibbo's) with espresso bars open to 11 or 12. Or there is the Peninsula Creamery with malted shakes, coffee, and a diner atmosphere open until 12.

Mountain View has several coffee bars, one upstairs in Books Inc. (the old Printer's Ink), and one roastery just around the corner from that.

If you want a nice cup o' joe, hit Khartoum in Campbell, Chris (the bartender also works at Boswell's in the Pruneyard) serves up a mean cup of fresh brewed coffee; being that it's a bar the atmosphere is good and open till at least 1:30am

My favorite place used to Café Babylon and it’s previous incarnation Kismet. But they are both long gone. There are three places that I know of that open sort of late.

1. Hookah Nite Café: open to till 2:00 on Friday and Saturday, and something like 10 or 12:00 during the week. It is a new place that took over Café Matisse. It is on South First Street between San Carlos and San Salvador. It is across the street from Camera One.

2. Hydration: I think it is open till 11:00 on most days it is on South third street between San Carlos and San Salvador.

3. Camera Café: I think it is open till 10:00 or 11:00 on most days it is at the corner of South Third Street and San Carlos at Camera Three.

Parking can be a bitch but there is free parking after 6:00 on Market behind the convention Center and above Camera Three. Do not park in the McDonalds parking lot. They will tow your car.

Pergs! Man I used to live in santa cruz for 4+ years. I totally miss that coffee shop! And the nuts who would tease those couples going into well within. And the motorcycles! Clove and regular cigs!

*sigh*

Good ol days