When you sold your websites was it fairly straightforward with how you had to transfer all of the materials over to the buyer, or is that something you just arrange behind the scenes with the buyer?
Also, I'm curious as to how you transferred the commission junction site - did you make it in such a way that the buyer could just substitute their affiliate id in for the deals?
For the sites I sold, the transfer was super easy. For the wordpress site, I ran a script to swap out the affiliate codes to the buyer's codes. The domain transfer was a GoDaddy push which took 3 minutes. I exported the database and used a login the client gave me to upload it to his hosting.
For the ebook site, I again logged in using credentials given to me by the client on his hosting and I uploaded the files, created the databases, and the site was online in 15 mintues.
From my limited experience, I would say that the lower priced auctions (under $2000) seem to be legit, but I have a feeling that the big ticket sites ($5000+) that either don't have verifiable histories (traffic, keywords, revenue) that sell are being sold back and forth between scammers. You can sell a fake site between 2 or 3 scam accounts for $3000, $5000, $7000 at a cost of a few hundred $, then sell it to an unsuspecting person for $10000, pointing to a history of being sold on Flippa as proof that the site is "legit"
For a legitimate site to sell on Flippa for a decent amount, it should have healthy organic traffic, preferably a high page rank, and verifiable revenue. But then the question would be, why would you sell it?