Cream of the Crop 

Cheeseboard Pizza- top of the list, most frequently visited, etc.  Simply awesome thin-crust pizza.  They only make one kind of pizza each day, always vegetarian, but it is consistently amazing.  Can't hurt to check out the Pizza of the Day page on their website, though.  My personal favorites are "Fresh corn, red bell peppers, mozzarella cheese, Bulgarian feta cheese, cilantro, and fresh key limes" and anything with their olive tapenade.  Slices are only $2.25, and they'll almost always give you an extra half slice, whether you order one slice or a whole pizza.  

Chez Panisse- right across the street from Cheeseboard Pizza, but a lot more expensive.  Downstairs is a set menu for dinner, costing $50-$100+, depending on the night.  The cafe upstairs is much more affordable (though still expensive).  This place is world-famous, legendary, genre-defining food.  The first thing my great uncle Ed, who lives in remote eastern Italy, asked me about when I told him I live in Berkeley, was "OH MY!  Have you been to Chez Panisse?"  It's a rotating menu, but you can't go wrong.  I love the goat cheese salad and the desserts.

Vik's Distributors- consistently voted the best place to eat in the East Bay in Zagat- this place rules!  Super cheap, incredibly delicious Indian chaat.  The samosas and masala dosa shouldn't be missed, though I generally stick to the daily specials, since they are a little healthier and give you a more traditional meal than the snacks. Viks is located at Allston and 4th Avenue, in West Berkeley.  Bring an Indian friend on the weekend- they make twice as many dishes as the weekdays, and it really helps to have someone to navigate the waters.  Plus, they will see someone they know, since the place is very popular with Indians.  Definitely a good sign. 

Cactus Taqueria- okay, so its not fresh-from-the-can, lard-based, authentic Mexican food, which I grew up loving in San Diego, but Cactus shows how great California-style Mexican food can be.  All fresh ingredients, awesome seafood, creative salsas, both healthy and tasty... I almost want to go right now.  Probably the worst thing for you on the menu is the best tasting- the hard tacos- but you can get the fish tostada if you want something a little lighter and healthier.  For the real deal Mexican food, you need to go to Taco Zamarano, on International Blvd. in Oakland.  Not much in the way of vegetarian food, though.

Koryo Sushi- the only place I'll eat sushi in the East Bay, at least if I'm paying.  If you want to take me out to dinner we can hit up Kirala, for some of the best sushi ever, but Koryo costs half as much ($15-20 instead of $30-40/person) and has high quality fish.  Family favorites are the Shrek roll, the Raiders roll, Amigo roll, and spicy tuna, of course.  They are open until 2am most nights.

Honorable Mention

Zachary's Pizza- Chicago-style deep-dish pizza.  It's like lasagna!

Razan's Organic Kitchen- if only they had better service and hadn't raised their prices.  How I miss you, Razan's...

Brazil Cafe- I wonder if the owner knows how much driving a bright-yellow Hummer in Berkeley is costing him in business.  Nevertheless, they are always busy, and the tuna sandwich is the best I've had.  The tri-tip is supposed to be awesome, too. 

Ajunta - the only reason it didn't make the main list is that I haven't been able to afford to eat at this place in three years, and Vik's is 93% as good for 20% the price.  Best Indian food ever, though.

Lanesplitter Pizza- one of the cooler neighborhood bar-pizza joints around.  I've only been to the San Pablo and University location.  Other bars worth visiting are Ben and Nick's, the Hut (warning: awesome dive bar), and Barclay's on College Avenue, and the Albatross in West Berkeley.  

Seabreeze Market and Deli- addictive fish and chips, good crab and calamari, too.  Try the crab salad sandwich.