There are definitely things about the 4310 that I like over the 3808, but the extra $500 is tough to justify (that's more than my current receiver - that I like - cost me). I do wish that the software upgrade for the 3808 still had the rebate, as I'd like a couple of the items in the $100 upgrade package.
Yeah the upgrade package is almost a must-do at some point, so you should only have to justify an extra $400. Honestly, it is a shame you missed the 3808, because that would have been the way to go for $400 difference. I just didn't think you could get it anymore for a reasonable price because they want you to buy the 4310 (maybe give AVS store a call about a 3808 for under $1k - I keep hearing great things about their store, but you have to call and I hate the phone so yeah). That said, $1499 for a 2010 model with no upgrade necessary is pretty dang good. It is going to be $1999 everywhere again soon I am betting...
The 3808 appears to have a fan, where as the 4310 doesn't seem to have any slots on the back for a fan.
No, there aren't fans in any of the Denons AFAIK. I hate fans more than the phone - I had a bad experience with the NAD brand AVR and their 3 fans throwing feedback into my speakers.
EDIT: There is a factory sealed 3808 from Amazon Warehouse that just says "box damage" - it is $1055, but maybe you could give them a call, find out about the box damage, and if it is nothing major, see if you could get it for a little cheaper since they were just selling one new for $999...