You could go literary:
The Bun Also Rises
The Red Bagel of Courage
Cyrano de Baguette
Panini of Dorian Gray
Pita and the Pendulum
The Chupatti Prophesy
The Name of the Rolls
The Old Man and the Schnecken
Or just plain old D’Ohnuts!
I don’t actually recommend this, as people will expect you to have Simpsons characters about the store - taking focus off of your goods - keep the focus on your delicious goods!
Hmm…
“Delicious Goods”
“Batter Up”
Or, just name it “Bakery” - but in a different language to make it sound exotic. You know, like, Boulangerie, or Panadería, or Panetteria.
buns3000
All Things Carb and Beautiful
Daily Bread (was that already suggested?)
Bread and Carcasses (only if you also sell meat, of course)
Seven Unleavened
Sourdough Pete’s Bread and Pastries
Some Enchanted Ovening
Top O’The Morning
Perhaps that would work if you were only selling muffin tops. 
You’re opening a bakery? How’d you raise the dough?
Bunzapoppin!
A Loaf Again Naturally
Loafin’ Naturally
Loafing Around
In Bread
I Vant to Be A Loaf
Pure Bread (Oooh, I actually like that one)
Meant to add, best of luck to you! (And let us know what you decide on)
The Hearthstone
Kneadin’ Dough
Wild Oats
First Federal Bake Shop
The Xyz County Independent Baking Company
Bread to Win
House of the Rising Bun
The Grainium (have a logo featuring a picture of a large-brained baker, or a diagram like this one, with names of your breads replacing the mental attributes on the lobes)
Rising to Your Occasion
The “Your” would be done in in a nice script to indicate you are thinking of the customer when you bake their loaves of bread and that its special enough for whatever meal they’re planning, be it a typical family meal or a more formal affair.
A Clean, Well-lighted Place For Yeast
I always liked the idea of “Yreka Bakery” (it’s a palindrome!)