Best Pie by the Slice / Whole in SF / East Bay
Crixa ... usually ... but it is more gallete-line
Stonehenge ... those anonymous pies at Berkeley Bowl
In that order.
If you are ever in Pinole, Bear Claw Bakery has the best classic pumpkin pie I have ever had in the Bay Area. They only sell whole pies though and you need to order in advance ... worth it.
I gotta try Sweet Adeline.
I agree with Nation's ... stick with the sweet potato (not pumpkin) and the lemon merangue. Skip the two crust pies like apple.
At one point ... many year ago ... The Grove in SF had great pie. Haven't tried it recently.
Destination Baking Co. in Glen Park has great fruit pies, usually sold only by the whole pie, usually only near the end of the week. I love his berry pies. They are not very sweet, and he might warn you of this (perfect for pairing with ice cream, then). Call ahead to see what/if they have in a given week.
I recently had a slice of apple pie at Mission Pie and it was fabulous--not very sweet, with apples slices that were cooked just enough to lose their crunch but still retain their shape, and a hint of cinnamon. Lovely crust. Whipped cream on top if you like. The pies are made by Joe, the guy who runs Destination Baking Company.
They also regularly have walnut and pumpkin pies. I haven't tried those yet.
This is a place I intend to support as they have a mission more ambitious and admirable than just to make great pie. Asherandeva said it well about a week ago: http://www.chowhound.com/topics/358012
2901 Mission (at 25th St.)