It really depends on what you are looking for.
(new) aftermarket parts can be had at just about anywhere online, just google what you are looking for (not google shopping as that will miss a lot of things) rc51parts.com (bensexcessbikes is the owner and a member on here) also has a few things like radial adapters and shock links and other things I am probably missing.
TygaUSA.com - Tyga Performance Carbon Fiber, Exhaust Systems, Billet CNC & More! has some nice carbon fiber stuff and a few other things like billet triples, and Glenn is a member on here (Rothmans). And yet another sponsor on here is Scott (cbr400rr)
Scotts Motorcycle Service - Servicing all Street & Crusier bikes ATV & Parts who has some nice things specifially for the RC51 as well.
(used) aftermarket parts: ebay, rc51parts.com, here in the classifieds or on other forums
Oem parts: Ben (rc51parts.com) is the best for quality oem parts, espescially if it's some little screw or clip that you don't want to spend $3.50 on at the dealer. If you need new or ben doesn't have it, this is the cheapest place I have found online for OEM parts:
Motorcycle Tires, Discount OEM Motorcycle Parts, Motorcycle Apparel, Motorcycle Accessories, Motorcycle Helmets, Motorcycle Jackets, Motorcycle Gloves However, I haven't had to order anything from them yet. I have had good results with
Motorcycle Parts|ATV Parts|Honda|Kawasaki|Polaris|Suzuki|Yamaha|Dealer|Wholesale Discount Prices in the past, but it's been a while.
If you are looking for used oem parts, that's kind of hit and miss. Plastics/tanks on eBay will cost you enough to make you want to just buy new, but some do come up on the forums from time to time. Most of us know what good plastics/tanks are worth though.
I would highly recommend doing business with either Ben, Scott or Glenn. All have met or exceeded my expectations and helped me out in the past. Remember that it's the sponsors that help keep the site alive, and that keep bringing us new parts like cbr coil conversion, radial adapters and other billet goodness.