I only spent about seven months in FL, so I'm far from an expert, but I did drive nearly 50 miles at least once a week to shop in Orlando while I was there.
Whole Foods Market in Winter Park (NE section of Orlando) on Aloma Avenue. They are the best spot I found while there for "health" food.
Lots of organics, tofu stuff, grains, fish (ok, and meat, not that I eat any of it), a nice array of vegetables and fruits, cheeses. vitamins and other unique goodies. Well worth looking up!
The Fresh Market (near Universal Studios, off of Conroy, irrc) is also a great spot. It's similar to Whole Foods Market, only not quite as "granola-ee".
But it is full of great food, fresh produce and some tasty sushi.
Another huge surprise for me while in Florida were the Target stores that had groceries! I can't remember the name of the street it was on, but it is near the Millenium Mall. The Target grocery store had nice produce and some great "whole food" selections mixed right in with the other stuff. I guess I was just impressed at the overall selection they had.
FL also has some nice farmer's markets, so be on the look out for those too.
I didn't spend much time exploring the downtown area or looking for those funky little neighborhood stores that every city has so I'm sure there are lots of treasures to be found as well.