I assume that any great reader out there has spent some time in bargain bookstores (or their close cousins, the garage sales). These are excellent places where one can pad out a collection, look for volumes that can no longer be found in the commercial libraries, or just hang around and see if anything cheap pops up. I estimate that about a good twenty percent of my current collection comes from the local bargain bookstores — and I'm not even much of a reader compared to other people.
That said, there are a few rules of thumb that I follow whenever I go through these places. One obvious expectation, of course, is that these bookstores almost never contain copies of the latest novels. Another is that the selections that you find here go through a certain shelf life (no pun intended) — a limited time of sorts, before they're packed up and "rotated" to other branches in search of buyers.
There are some less obvious aspects, though. For one, there's the fact that you can expect a bookstore's selection to cover only publications from the last ten to fifteen years, beyond which it becomes much harder to find a specific book. Bargain bookstores in major metropolitan areas are likely to see a faster turnover, perhaps covering only books from the last five to ten years. Provincial areas are more likely to see older volumes; you can even catch some original Mickey Spillane or Agatha Christie if you know where to look.
After that, it begins boiling down to the various genres and classifications of periodic literature, all of whom have certain discernible patterns if you spend enough time in these places. I'll put up a few of these observations from my corner of the shelves:
General Fiction - Every bargain bookstore's selection of novels is, by definition, a "general fiction" section, usually because the salespeople don't go through all the trouble of putting these things in the right bins. Be prepared for a generous helping of books that would otherwise belong in specific genres (in fact, if you read nothing but general fiction, this is a good opportunity to broaden your horizons). Expect a lot of Sidney Sheldon, Michael Crichton, and a bunch of authors that you've never heard of (and probably will never hear of again).
Mystery - The Mystery selection of any bargain bookstore is usually rather extensive, and for good reason: The essence of these novels lie in the mystery itself. Entire plot developments, secondary storylines and red herrings go into these books, which means that, although they may make for a good read the first time around, they're usually worthless for a second go. As a result, a lot of these books land on the bargain shelves. If you're looking for a specific Mystery novel, these bookstores are usually a better option than the high-profile branches. Anything that was published within the last ten years can probably be found somewhere here.
Horror - You're likely to find about as many of these books as Mysteries, because they share a similar weakness: A Horror novel simply isn't likely to be as scary the second time around. Another fact is that, realistically, there aren't that many popular Horror authors on the market, which means that you can probably call this the Stephen King section with some degree of accuracy. The fact that his works get reprinted on a regular basis doesn't help... although these are a great place to fill out your King collections with very little prompting.
Fantasy / Science Fiction - For some reason, bargain bookstores never seem to have any good selections of "imaginative" literature. My guess is that the people who buy these books are more likely to keep and reread these, which limits the number of volumes that make it to the secondary market. There's also the fact that some of the best examples of this genre were either written over twenty years ago (Weis/Hickman, Donaldson, Asimov) or only very recently (Gaiman, Martin), and the result is a fair-sized gap when it comes to bargain bookstore shelves.
Romance - Interestingly enough, there are quite a lot of Romance novels on the shelves, but this is not for a lack of rereadability. Instead, I blame a strange compulsion that comes over those who read Romance novels, one that convinces them to pick up books upon books from this genre, and results in bloated home collections that don't mature very well as one gets older. This gets a lot of people to give away or sell their "weaker" specimens, and gets a lot of bookstores picking them up for resale. As with Stephen King, only expanded to a range of authors that includes Steele, Lindsey, Brown and others, this is a good place for completists to look. Just remember that whatever you buy here may just as easily make its way back once you tire of it.
Self-Help / Inspirational - I find that the best self-help books never make it to the secondary market, which implies that the examples you see here are either excess copies of famous writings, or utterly useless volumes that couldn't find a hole in the ground even if they knew where to dig.
Educational - The vast majority of educational books in bargain bookstores are outdated, but less so than you may believe. Usually these books become outdated because 1) they rely on outmoded methods or tools, 2) more relevant historical events have occurred in the interim, or 3) renewed editions have emerged. As a whole, the basic learnings that they carry are usually still worthwhile, although you'll need to be careful enough to tell the difference. A book on graphic design will still teach you graphic design, even if we're now using Adobe Photoshop CS instead of 4.0. Programming languages are the primary exception that comes to mind, though, if only because the use of Turbo Pascal has diminished greatly in the last twenty years.
Health - I usually suggest that people try not to pick up Health books that are even so much as five years old, because you can never tell what surprises have been discovered in the meantime. Besides, why not just consult a doctor, nutritionist or personal trainer?
Religion - I find that most religious books land in bargain bookstores because they don't sell too well in ordinary places. Sadly, a lot of these books tend to be reactive — Remember all that literature that came out "debunking" The Da Vinci Code? — which really limits their shelf life. In fact, any religious book that relies heavily on its current status quo makes for very out-of-touch reading. (I once picked up a book that predicted that the Rapture would take place in 1981, just for a laugh.) If you must pick up a Religious book from the bargain bookstores, look for something inspirational; there's no shortage of them, and they usually never become outdated. Bible studies are very nice as well.
Children's Books - I see bargain bookstores as a great place to find good children's books, because kids will eventually outgrow their favorites at some point, and these can easily be passed to a new generation. Hardcover books are usually of far better quality than the paperbacks; Dr. Seuss and Shel Silverstein can be found among the shelves here. I would suggest avoiding the paperbacks entirely, if only because most of these seem to be little more than licensed knockoffs ("Shrek Counts to Ten") or series of dubious quality ("Animorphs", anyone?).
Magazines - There will never be a shortage of men's magazines and women's magazines inside bargain bookstores, because their circulation is so extensive that we end up with a ton of excess copies. What that means is that you can take this opportunity to fill out any issues of Cosmopolitan or FHM that you lack. Beyond that, the only other magazines that our favorite bargain places are likely to have in high supply are those titles that nobody reads. In Manila, it seems to be Hot Rod, or High Times, or Fangoria.
Comics - The only comics that show up on the bargain shelves are, strictly speaking, those comics that belong on the bargain shelves. Bookstores have it worse, since they usually get the throwaway dregs from the more qualified comic stores, which results in only the most obscure titles or the most banal single issues. If a bargain bookstore has comics available, that usually implies that there's a comics store nearby. I highly recommend that you find that other place instead.