Bottom line is "If it sounds too good to be true, it usually is".
Don't get me wrong, I've bought and sold over a dozen bikes on the internet (Ebay, Craigslist and Cycletrader) in the last 3 years. After a while you can sniff out the real deals from the scams (usually). I ALWAYS ask if the bike is available for viewing, whether I can get there or not; if I get some song and dance about it being in another state from the one advertised, I walk; if I get some song and dance about not being willing to do escrow or paypal, I walk. If I get REAL BAD grammar or misspelling to my emails, I walk (a LOT of these scams originate overseas). Mostly, I get familiar with the prices of the bikes I'm interested in (KBB.com, NADA.com

: these sites arn't the be all/end all for pricing, but they do give you a good feel for RELATIVE values.
Most of all, I try not to be greedy....if I'm looking at a two year old Hayabusa with 1500 miles listed for $3800 bucks; well, if I believe that's a real deal, I guess I deserve to get scammed. Bu the same token, last year I bought a 2003 YZF 600R with 90 miles on the clock for $3900 on E bay; before I bid, I emailed the seller that I wanted to talk about the details of the bike (it had been dropped in the driveway; scraped lowers, bent clutch lever and a busted turn signal) I talked to the seller and got a feel for whether the guy was legit, and he sent me a boatload of photos of the bike and damage. I made a bid, was the only bidder, and the bike and title were delivered as promised. ( I fixed the issues, turned around and made $1500 the next week).
The bottom line is do your homework
on the bike and the seller, and don't get greedy. If the seller won't talk to you on the phone, or the parameters of the deal keep changing, it's prolly no good.
Meebe those that have extensive onlinbe bike buying experience could put together a sticky thread on "Buying a Bike Online".