in your case, like you said, what you want will rarely be available.
normally, i like craigslist first- generally the best deals are to be had there. not much to choose from though, and sometimes you'll have to travel a fair distance and the commutes suck sometimes (i've had to go to brooklyn many times, upstate, ext.) the crackheads and weirdos are a blast to haggle with, though.
then ebay- bigger selection of used stuff, and often good deals, always fair prices to be had (for the most part.) the annoying thing is auctions, though they often yield good prices, sometimes (like the MIM strat i THOUGHT i was going to win the other day..) someone else REALLY wants that item for auction, and you just cant have it unless you're prepared to pay almost retail prices.
retails stores, even on used stuff, its usually not that great. pedals that retail at $179 they'll be selling for $159 used, when ebay their every day price would be $100-$120. that said, one great place is guitar centers used section online- as we all know, GC employees mess stuff up often. i have noticed that anything up there for a decent price is gone really, really fast. only look if you've got the cheddar to throw down, because its very frustrating missing great deals!