For all our area has, it sure is lacking in haunts for the night owls among us. Short of Denny's, there aren't a lot of options. I have qualified "late night" as places that were open daily past 11pm that weren't just bars.
Menlo Park's The Oasis Beer Garden on El Camino is usually open until midnight (give them a call before you head out. I was told they might close early on a slow night). They have a decent selection of your standard bar fare: burgers, hot dogs, fries, and pizzas which I have found to be only fair. However, they do fry a mean onion ring. The atmosphere is loud and racous, there are plenty of booths and tables and the crowd seems to be largely Stanford students.
For a bit more than bar food, there's Frankie, Johnny and Luigi Too also on El Camino in Mountain View. They are open until midnight Friday through Sun. and until 11pm Monday through Thursday. They have a good selection of all the Italian standards such as pasta, pizza, antipasti and salads. Prices are moderate, portions are large but parking can be a bit of a hassle. Fun atmosphere.
If you're a night owl with a sweet tooth try Neto Cafe at the far end of Mountain View's Castro Street. They are open until midnight Sunday through Thursday and until 1am on Friday and Saturday. They have Mediterranean and European cakes, tarts, pies and mousses. The Rugalach is a must-try though a bit bigger and denser than what you might be used to. They do have coffee drinks (try the Turkish coffee) sandwiches, salads and Mediterranean dishes as well. A bit pricey on the desserts but at midnight and with free WiFi who's complaining? Cute European cafe atmosphere at the end of the Castro Street hubbub.