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San Jose area does not have a huge late night dining scene, unless dennys, or weinerschnitzel is your thing, but, Downtown is your best shot.
The number 1 late night joint in san jose, hands down is Original Joes(301 S. First St., San Jose, (408)292-7030). They're at the corner of 1st and San Carlos ave. They're open until 1am, and they serve a combination of italian, and "other". One favorite is the chicken parmesean, make sure to ask for mushrooms on top. mmmm Their pasta is also really good, including the ravioli, it tastes VERY fresh, and yummy.
Also downtown, on san carlos, and 4th is La Victoria(140 W San Carlos St, San Jose - (408) 298-5335). This no frills taqueria is a favorite of the local bar goers, and San Jose State Students (its smack dab between campus and the bars. They're open to at least 1AM, probably later on the weekends. Make sure you grab a container of the orange sauce.
Finally, and also in DOWNTOWN SAN JOSE, the newest exotic destination is Morocco's Restaurant located at 86 N. Market Street.One of the few places offering fine dining until 11:00PM 7 days a week. RSVP are highly recommended at 408-998-1509. Feel free to check out this little gem at www.MoroccosRestaurant.com and the entertainment that comes with it by looking at their calendar of events at http://www.moroccosrestaurant.com/eve.... Their $4 Sangria night and Guitar wednesdays or $15 Five wine flights Thursday with a free appetizers makes it a favorite for good athmosphere seekers.
In Cupertino, Pho Hoa(1080 S. de Anza Blvd., Cupertino (408)366-0544) is open until 2AM (recent change! the used to only be open until midnight). They are right next to the Britania Arms, which is a popular bar. It is clearly a "fast food" type pho place, but the prices are reasonable, you'll never left hungry, and they're open late :)
In Milpitas, your best bet is to cruise the Milpitas Square. Milpitas square is an asian mall, with a large asian grocery store as its anchor store. Some restaurants don't even bother putting out english menus! To get to the Milpitas square, from highway 237 exit Mccarthy Ranch, turn AWAY from mccarthy ranch (towards the south side of 237), and turn left at the first stop light intersection, at the gas station. Continue until that street dead ends (about 1/4 mile), and enjoy :)
In Fremont (Milpitas/Fremont border), a good place for late night eats is: Cafe Ophelia - On Warm Springs Road (just off of Mission Drive.) This has wonderful hot pots; great full dinners (Taiwanese/Asian taste); wonderful teas and coffees. It is open late and very good food. Several types of dinner served:
a) Hot Rock grilling - raw meat that you cook on a hot rock that's brought to your table
b) East Asian versions of western entrees - spaghetti, chops, etc.
c) Pan-Asian dishes - eg. Pineapple rice
d) Hot Pot- you cook stuff at the table in a vessel holding boiling soup, some specialized ones with herbs
None of their food is traditional, instead they're aiming at a kind of citizen-of-the-world fusion. The restaurant is nicely decorated with some nice small sculptures, nice tables in the room. You can come just for tea and snacks, bring the family, or enjoy a full dinner for a nice evening out with your significant other.
If you are dying for a midnight sweet tooth binge, check out the Donut Wheel (10250 N De Anza Blvd, Cupertino - (408) 252-8193). They are down the street from Apple, and Deanza College. This place never closes. I'm not kidding. They're "Open" sign is stenciled onto the window :D If you go within a couple hours of midnight, ask them if they have any warm donuts. Whatever they have warm, get it. Its absolutely wonderful, especially the donut holes, or apple fritters. If they don't have anything warm, you still can't go wrong. This is a cash only place, and its usually full of college students studying, or at least pretending to study, so you may have a hard time getting a table to sit at.
A fastfood chain that many consider exceptional is In N Out Burger. Locations like at El Camino Rl and Grant Rd in Mountain View are open until 1am, and 130am on Fridays and Saturdays.
A small chain of Denny's like coffee shops called Carrow's is also available 24 hours. Carrow's is often considered far better than Denny's. Breakfast items are available 24 hrs at Carrow's.
Good Luck, and good late night eats :D