What we think we'll do is spend most of the week in a cheaper hotel somewhere, and splash out for a night or two somewhere a bit special - some classy hotel with a room with a view, good food and a few well made martinis
In that case... stay at the
Chateau Tivoli. It's a couple of blocks from the Alamo (and the painted ladies

) and the interior decorations are amazing. Try to get a weekend night, so you get the hot breakfast in the morning (with champagne!) Very reasonable prices, too, amazingly.
On the food side - we're not picky

It'd be great to hear from people about any of the restaurants that only 'locals' know about. Kind of a mythical thing I guess, but the sort of places that don't look like much, but do great food.
Ah, in that case... like burritos? If you go to the Asian Art Museum (or heck, anywhere in the Civic Center - check out the city hall!), on Hyde St., walk north past UC Hastings College of the Law to Golden Gate Ave, and go left. There's an awesome Mexican joint there, with the best burritos. I have no idea what the name of the place is, but you can't miss it (it's right next to the Vietnamese restaurant if you're having difficulties - it's across from the giant parking garage/retail space under construction).
Hamburgers? Fries? Fries with cheese and chili? Split hot dogs? Go to the Castro. Enter a joint named Sliders. Eat up!
Sushi... there's a place on Powell, a couple blocks north of Union Square. Awesome sushi, not too touristy, despite it's location. You also can't go wrong with the sushi place in the Castro. In fact, you just can't go wrong in the Castro as far as food is concerned.
Pizza? Hit Uncle Vito's Pizza, just off Powell St. on Bush St. (Take the cable car and hop off at Bush St if you don't feel like walking!) There's also the Sausage Factory in the Castro (told you, you just can't go wrong!)
Italian? If you like garlic, you're gonna love this place. The Stinking Rose, on Columbia in the Little Italy part of town (near North Beach). Either take the cable car, and walk all the way there (it's fun!

) or take the bus on Stockton (that's the street the Apple Store is on, so you will definitely be in the right place

) up to Union Street, and walk there.
Dim Sum? If you want a more fancy, nicer location, and best-tasting, you gotta pay for it

. Where? Yank Sing, located in an office building on Spear St. (take the old F line north along Market if you want some fun! You can also take the F line to the Castro, too!)
But if you don't mind a run-down place that looks iffy, but has delicious food for INCREDIBLE prices, hit Dol Ho on Pacific St. between Powell and Stockton, just off the tourist parts of Chinatown. You will see locals there, no question about it (take either the Stockton bus or the cable car up there).
BOBA TEA! I loooove those drinks! Quickly's in the Castro is the easiest to access - stop by there after eating your hamburgers at Sliders! But there are better... My favorite is Sweetheart, on Grant St. (it's right in Chinatown, just walk through sightseeing, you'll spot Sweetheart eventually). For a more, ahem, interesting one, check out Chamalyn's. It's a bit out of the way, but if you don't mind that, you can take the bus on the Mission all the way there. It's on 19th St. You can check out Dolores Park while you're there, too.
Thai? Check out the place at the corner of Larkin and Geary. Awesome Thai food, and even more awesome fried rice! Good prices, too!
For something not-so-local, go check out the mall at the Powell station. Check their food court - it's unlike most food courts. It's the upper end of food courts.
There's os many great places to eat. As someone who lives in San Francisco, those are the "local" places you really should check out.
EDIT: And to add... I don't go to many bars, but I can suggest one! It's the La Trappe, a Belgian bar. Located on Greenwich St., take the cable car there, the bar is literally right next to the track. Just hop off and enter! Great atmosphere, very local place. Great food, too! Try their chipotle mayo with fries! Yum! Decent beer selection, of course.