Whether you are a fan of the big box theaters or the independents, we've got some great choices in the area.
As far as the independents go, I am a big fan of the Palo Alto Square CineArts. It's a nice hybrid of the big theaters with its creature comforts yet is still artsy with smaller theater charm (2 screens). Parking and seating are plentiful.
Menlo Park's Guild on el Camino is a sweet little single screen theater. It's the only place I know around that has shown The Rocky Horror Picture Show. It has a racy history, built in the late 1920's as a burleque house and coverted into a movie theater in the 1940's.
Downtown Palo Alto is blessed with both Aquarius and the Stanford Theatre. Parking can be hairy at both but they are worth the hassle and if you want to make a night of it, come early and grab a bite first. Aquarius has a Midnight Madness series from mid-summer to mid-fall and features classic and cult films with games and giveaways on Fridays and Saturdays. The single screen Stanford is legendary. First opened in 1925 and then restored in the late '1980's by the David and Lucile Packard Foundation, it's now owned by the Stanford Theatre Foundation and shows classic Hollywood movies. 7:30pm shows feature a live organist on their famous Wurlitzer. The interior is breathtaking. While poking around before the show, check out the annex with the vintage movie posters and other goodies. At $7 for an adult ticket, it's also a deal. Tip: buy a $24 Gift Certificate good for four admissions.
The new Century 20 in Redwood City is about as clean/modern as it gets with more screens than you can shake a stick at. This is the place to see the latest Hollywood blockbuster. It boasts free parking with validation (though it can sometimes be tough to find around there) and is smack dab in the heart of the newly revitalized downtown. Expect to pay a premium, however, with tickets hovering at almost the $11 range. It can also get pretty packed with a high school-age crowd so set your expectations accordingly.
Mountain View's Century 16 is a somewhat dated older theater a bit off the beaten path near Shoreline. What I like about this place is yeah, you can catch all the Hollywood films but they occasionally toss in a foreign and/or independent flick as well. It also gets a bit nutty on the weekends (particularly Friday night, it seems) with seemingly-endless throngs of teenagers. I prefer to hit up the Century 16 for a matinee and then take a stroll around Shoreline Lake and maybe work off my popcorn and soda but renting a paddle boat. Good times!