Things I regret come not so much from them being bad purchases, but because I have barely or never used them for anything worth the money spent. Back in the days when I had money (and no girlfriend/wife) I bought a lot. Leading to quite a few regrets...
1) RIFTS series by Palladium (I don't own all the books, but quite a few). I played this a few times in high school, liked it, but could never get anyone else to play. I still have them because I like the story, but would readily chuck them if I needed money.
2) 3.0 WotC Splatbooks. I think I've used one feat from Sword and Fist (Monkey Grip), haven't used any of them since. Especially since the Complete series came out.
3) DM-related books (Deities and Demigods, Manual of the Planes, Stronghold Builder's Guide, BoVD). I don't DM enough to make use of them. The one time I recently tried, I was going to use the Greek Pantheon, and so would have used the information on cleric domains and godly fluff, but the crunchy stuff would have never come into it. The other three I just liked and bought to be a completist. Again, would sell them in a heartbeat except for Deities.
4) Mongoose "Quintisential" series. I have a few of these, mostly inspired by my fondness for the old 2e class handbooks from TSR, but again have used one feat (Light Arcane Armor from the Wizard's book). Probably will sell most of these now that 3.5 renders them obsolete and my group would never use them.
5) The first 3.0 Kalamar Book (I think it was called Player's Guide). A little misleading, as I thought it was going to deal more with playing in the world rather than describing the world. Never bought another one of these, but now my group may be playing in this world soon so I'll either keep it or sell it to my DM for cheap.
6) Hackmaster PHB. Again, I liked it, but I bought it mostly because I'm a Knights of the Dinner Table fan and not because I thought I'd play it. Might sell this too. Still, all love to KenzerCo.
7) Savage Species- nice idea, but way too complicated to deal with in play. I think I sold it... it's been so long.
8) Psionics Handbook- I never liked 2e psionics, because it seemed more suited to people who like number crunching rather than playing. I tried out the 3e book, but a lot of it just didn't make any sense to me after multiple read-throughs. Sold it, never got the new book, never will. Nobody in my group uses it, anyway.
9) Fluid's E-Tools. By far the crappiest piece of software I've ever owned. Very slow, lots of errors, hard to use. Code Monkey did a very good job overhauling it, and I would recommend their version except that they're coming out with something new in the near future that will combine E-Tools with other material.
As for some others mentioned already, I like BoED. I used it to great effect recently playing a paladin in the World's Largest Dungeon, and would have used more of it if my character had survived longer. Unfortunately, his death came partially from the restrictions of being an exalted character, so I quickly dropped using it for any other characters in WLD. Also, my group likes the Player's Guide to Faerun. Our DM especially thinks it balanced out some of the feats (like Spellcasting Prodigy). But I understand, gustum non disputandum est (taste can't be disputed).
