There isn't a Trader Joes in Berkeley... do you mean the one on College (Rockridge)? I haven't been to that one, since the parking situation is a joke, but if you're taking BART it's fairly convenient.
If you're in Alameda, I'd hit Trader Joes at Southshore. It's a lot closer. There's a farmer's market on Tuesday... Wednesday? Don't remember. It's small but not bad. There's the marketplace out in the old downtown area (I'm bad with street names)... right near the bridge. It's pretty cool, but pricey. There's also a farmers market on Friday in old downtown Oakland near the tunnel that is good. Better during the summer than the winter. Definitely get in and out before lunch though, since the office buildings flood it at lunch time.
I do my natural food shopping in Oakland, since they finally gave us some options (drove to Alameda for years before that). The Saturday farmer's market at Grand Lake is fabulous, but if you want parking get there by 9:30. There's a Trader Joes right around the corner, so it's one stop shopping. There's even a natural food store on that same block, although I've never checked it out. After I do those two stops then I swing by the Whole Foods on the corner of 27th and Harrison, which is on my way home, and get what's left. That WF has plenty of parking, unlike the one in Berkeley.
Everybody raves about Berkeley Bowl, but honestly I don't see it. I've been in there once and wasn't terribly impressed. Definitely not worth the hassle of driving and parking in Berkeley, IMO.
For bulk foods I go to the Food Mill in Oakland. I like supporting the local guy, and they have the best selection I've found. From bulk herbs to all your kitchen spices and even bulk honey and maple. Right nearby that is Farmer Johns which is a pretty darn nice regular locally owned supermarket. They don't really concentrate so much on the organics, but they do have good meats. Andronicos is also pretty nice, but like Farmer Johns they don't concentrate on organics.
I've heard great things about Rainbow, but they're an entirely vegetarian store, which really makes it not worth the trip for me.
And of course, being in Alameda, you have access to the Ferry, which means the Ferry building markets in SF. The Saturday market is excellent, although it is expensive. Prather Ranch and Cowgirl Creamery both have shops in there and are great sources for local meat and cheese. But, alone they're not worth the trip, since Prather is at the Grand Lake farmer's market on Saturday, and WF carries Cowgirl Creamery.
Oh, and all the TJs in the area have the same pricing. There's not much point in shopping around on that. And the one in Alameda is the biggest one I've been into, both Oakland (Grand Lake) and Emeryville are smaller.