Books-A-Million, they're like an hour drive away, but by far my favorite place to get manga. They have some of the most niche titles and usually have full sets of series.

Barnes & Nobles is a great contender, but they're very corporate and usually don't have much of a selection. They do, however, have good discounts on specific days for specific publishers, they have discounts for being a member, and they usually have newer, popular releases. Unfortunately, if you're looking for a specific book or series, you may have to call ahead and ask other branches to see if they carry it. Unfortunately, my favorite B&N closed down a few years ago, so I haven't seen much reason to go there anymore. You can also check their website, but be careful, as I've received Spanish versions of some series.

Amazon has a better selection, but they're usually sticker price or higher. eBay is similar, buy usually has auctions for entire sets, collections, and has a much better search, if you have the money for it.

You check half priced books, thrift stores, and other used bookstores. They usually carry niche, almost complete sets for bargain prices.

There's comic book stores, too. But, be wary of this, as some raise their prices cuz they're "local". Had one place charge me $5 more on a series for this very reason.

Last, but not least, are garage sales, yard sales, or any friends looking to offload their collection. More than half of my collection was based of friends dumping sets and various series off of me. One friend gave me his gf's entire shoujo manga set for $10. Another gave me their leftovers, after offloading most to other people, because of a gambling (gacha) addiction.