Virginia Bakery
Virginia Bakery is a nice old-fashioned neighborhood bakery that has been in the same location for a long time. They have a big glass case showcasing their tasty treats, which are very attractive. The cookies are great! Sometimes they offer free samples of the cookies and other items. The cakes are also excellent, but be warned that they come with a thick buttercream frosting that can be a little too rich even for a frosting lover. Also, if you are looking for organics or other crunchy granola stuff like you find elsewhere in the Gourmet Ghetto, you may want to stay away since I'm pretty sure they use all kinds of food coloring and maybe preservatives, like most (non-Berkeley) bakeries. As I said, the place is old-fashioned. And good!!
Dark Carnival Of Crime
The name pretty much says it all here. It's hard to categorize the books they sell, except to say that they are 'dark'. There is a lot of mystery, crime, horror, science fiction, fantasy, etc. The selection is great (in those categories), and the store is friendly. You can get on a mailing list or check their website for special events like book signings, readings, and parties. It's a neat store to check out if you like the types of books mentioned above or if you are a goth-type person looking to meet other weirdos.
Friends of the Berkeley Public Library Bookstore
This place is just a little room under the orange parking structure between Channing and Durant. There's really not much here to speak of, but if you are in there anyway (e.g. if you parked there, or you're going to Revolution Books), you might as well stop in and see if there's anything good. Mostly I've found the selection to be not so great, but the prices are pretty cheap, and every now and then, if you stop by often enough, you may get lucky and get a bargain. Plus it's nice to support the library.
Other Change Of Hobbit
This is an extremely nerdy bookstore specializing in science fiction and fantasy books and comics. I can't emphasize enough how nerdy it is. The employees are among the nerdiest people I've ever encountered. They are also extremely helpful and they know their stuff. I once went in looking for what I thought was a pretty obscure science fiction book, and although they didn't have it in the store (despite an impressive selection), the guy I talked to knew all about it and offered to order it for me. This place is like paradise for nerds.
Alaya
The people who work here are super-friendly and extremely helpful. They seem geniunely interested in talking with you (it helps that there usually aren't a lot of people in here), making it a nice experience all around. This is a pretty big store, and it's got a good selection of all sorts of books (most about various world religions) and metaphysical supplies, gifts, etc. There's definitely a hippie/New Age vibe in here, so it's a good place to bring out of town visitors.
Sotto Voce
Sotto Voce has some cute little gifts and jewelry items, but I've never felt totally comfortable going in there because the clothes come in tiny sizes and so do the employees. I think it must be part of the whole European thing that this store is going for -- fat Americans not welcome. The employees were never rude to me or anything like that, but I just felt like I was kind of invisible, and honestly they had no reason to pay attention to me because clearly I wasn't going to buy any clothes. So if you are a small person and you like buying cute little European fashions, you would probably have a good time in this store. If you aren't, you might not.
Harmonique Garden
Harmonique has a nice selection of home accessories and jewelry that you won't find in other places. It is an upscale store, but very friendly, and there's a range of items from small, relatively inexpensive gifts to large, expensive furniture pieces. They also have a mailing list you can join to get invited to occasional special events at the store. The only reason I give it a 4 rather than a 5 is that I kind of wonder whether the employees work on commission. One time I was buying these two floor cushions, and one of the people at the counter asked whether I wouldn't want to buy three cushions instead, because it would be "more zen". I have no idea what that meant, but I was a little annoyed at the sales pitch. But I think I only noticed something like that once, so maybe the person was just trying to be funny or something.
Two Star Dog
This store has a good selection of clothing in a nice range of sizes, mostly made of hemp but some organic cotton. The clothing is of good quality, and although it is a little pricey, it is not any more than what you pay for hemp clothing elsewhere. Also, the clothing here is nice, like stuff you could wear to work, showing that you can wear hemp and not look like a stereotypical burned out hippie (not that there's anything wrong with that). The store also offers some nice gift items including hemp stationery, a nice selection of purses and bags, and also some pro-hemp books and literature. Highly recommended.
Poppely
This store is in a very convenient location near the corner of University and Shattuck, so it's tempting to stop in if you're in a pinch to find something dressy. I did this a few times, and each time even though I was desperate, I just couldn't find anything I wanted to buy. The dresses range from 80s Businessy to New Age Frumpy with not much in between. There's a decent selection in terms of the number of different items offered, but it's just that I didn't like any of them. I think this place must cater to older women, but even in that case, it would have to be older women with strange taste in dresses.
Books Out Loud
I was skeptical about whether there was a need for a whole bookstore devoted to books on tape, and whether such a store could succeed (especially in what must be a high-rent space). But actually it turns out to be a pretty cool idea, and it's nice to see such a big selection of them all together. It seems like books on tape are making a comeback. A lot of people I know are listening to books on tape while knitting, so maybe the two fads are intertwined. Regardless, you should give this place a try, even if you don't think you are interested in the whole concept.