I totally understand your rant. I rarely stop at Flea Markets any more, I usually hit those during the winter when garage sales are out of season. I've seen prices higher then Ebay sometimes from Flea Markets. And thrift stores, again I stop at them once in a while, but most of the time I find just sport games.
I always hear about people still finding deals at both of these places and it doesn't hurt to check in on them, you might get lucky.
How I get the finds I do takes a lot of driving around and foot work for 3 days at 6 hours each day. Part of the fun is the hunt, I have a ton of competition in my area, there's more and more resellers every year, I'm shocked I can find anything anymore. Heck I'm finding more and more garage sales where they want top retail prices on games, nothing ruins my day garage sale'n and see a table full of games at high end ebay prices. 
The only tip I can give you is hit as many sales as you can, it's a numbers game. out of the 50 sales I hit maybe 15 will have games, and maybe 2-3 will have good retro games. 
I live in a pretty rural area in Missouri. I'm 10 miles from the closest town which is Farmington. I drug my youngest daughter out with me this past Monday. Drove 10 miles to Farmington, then south for about 20 miles to a town called Fredericktown that had a listing for two thrift stores and a Goodwill. Well, the first thrift store is gone. Thanks for the updated listings YP!
Drove over to the Goodwill, only to find that it's a regional office and not a store.
Around the corner was a thrift store. The best thing they had there was Ecco for PC. Meh...didn't bother.
Now, headed north for 35 or so miles to another town called Bonne Terre which "supposedly" has three thrift stores. I already knew one was there because I picked up Def Jam Vendetta there. Well, the second one in the center of town was long since gone and the other one in the Bonneville Plaza was closed. It's been closed the last three times I drove past the damn thing!
Headed back south and stopped in Desloge at a pawn shop. They had some nice stuff, but had it priced at eBay levels. It took all of two minutes to see I wouldn't be buying anything in here. They wanted $55 for beat up DSi's for @##$ sake!
Drove further south (working my way back toward home) to another town called Park Hills. Didn't see anything at the pawn shop that I wanted/needed. The two thrift stores were both closed (notice a trend here?) and the local junk shop Jose's didn't have any electronic device newer than I would say...1940ish??? The mom & pop store was also closed. I guess Monday is the new Sunday around here. Not that I buy much there anymore because they have been raising their prices where it is nowhere near reasonable. On the way back to Farmington, I stopped in one of those antique/flea market indoor stores. Not a single game to be found there.
Headed back to Farmington and stopped at Goodwill. The only thing I was interested in there was a copy of Hot Shots Golf for the PSP which was a Greatest Hits version. Unfortunately, some douche let the insert ride up about a half-inch over the top of the case and it was pretty much obliterated. I passed.
It was then that I hit up the Farmington Gamestop which is the only one within 40 miles and my bud Dave runs. He's a good guy and all his staff are gamers. No hipster douches here. Ended up with Duck Tales new for $10. Also picked up used, complete & like-new condition copies of Aliens vs. Predator and Medal of Honor for the PS3. They also had a nearly complete copy of Dragon Age Origins collector's edition for the PS3. All it was missing was the map. After I got the sticker residue off the outer sleeve and wiped it down really good, it looks pretty presentable. Got that for seven bucks.
Moral of the story? I drove close to 100 miles total and spent about six hours of my life, only to end up back at Gamestop where I got some decently priced games in great condition. Next time, I'll just drive my ass up to Chesterfield where there is a big V-stock store or browse eBay. I still have one more of those storage places that doubles as a weekend flea market in Farmington to hit up this coming weekend and one of the local pawn shops where I picked up the Zelda and Mario Wii games is about a half-mile from there.
But man...it sucked doing all that and basically coming home empty-handed.
