Deals can be found all over, usually the only place I don't often buy SNES from is ebay because the competition over there is too intense.
Craigslist / Local - Will net you the best deals, but finds can be few and far between.
Amazon - Good because you can use trade-in credit on 3rd party sellers.
Retro Stores - Sometimes good for uncommons with lower sales rankings
Also Lowballs, CAGs, Nintendoage people, etc.
For recommendations, what genres are you into?