(I really despise the terminology, btw--it's sooooooooooooo gimmicky!)
I've never had Pinkberry or Red Mango, but I have had some frozen yogurt at different places:
Gelayo Gusto - Mountain View, CA - While they serve mostly gelato, they also have a frozen yogurt bar with quite a few toppings offered. I usually prefer plain yogurt flavor, and I thought that it was decidedly ok. Not bad and it's close to my office, so if I ever feel the hankering for some frozen yogurt, I know where to go.
Fraiche - Palo Alto, CA - I LOVE this place! It's so yummy, especially since everything offered is organic and locally-grown, and the yogurt is made fresh every morning! It's a little bit pricey, but it's quality stuff. They don't have a buffet of haphazardly picked toppings (like 10 different kinds of cereal), but they do have lots of fresh fruit, nuts, and a slab of (Scharffenberger?) chocolate that they shave off onto your yogurt, if you so please :)
And that's about all I have, as far as the places I've tried. I'm figuring this can be the comprehensive "Bay Area" frozen yogurt post. While I'm perfectly aware that another thread exists asking for Fro-yo recommendations (http://www.chowhound.com/topics/405026 a la Pinkberry, though), this should serve to be more up to date, as an increasing number of frozen yogurt joints pop up everyday here.