If you've got an Apple TV, or you're considering buying one, then this post is for you.
I bought my Apple TV to watch content that I've downloaded over BitTorrent on another Mac - quite a specific use case. I've been using aTV Flash for about 9 months. It's been pretty good, and improving, but it cost $50 and there's a free alternative called Boxee which I checked out over the weekend. Here's a brief comparison (v3.5.1 of aTV Flash, 0.97 for Boxee).
Installation: Both solutions were pretty easy to install. Maybe Boxee was slightly easier, because there were a few areas where the process was simplified. But not much to choose between them.
Streamed content: Boxee won this round too - in fact I think Boxee is mostly designed with streamed content in mind (much bigger in the States than here in the UK - see Hulu). But not much good for me as I don't watch much streamed content.
Interface: aTV Flash just extends the existing Apple TV menu, Boxee creates a completely different interface (which you still reach from the Apple TV menu, existing functionality is protected). Personally I prefer simplicity, and this is quicker too, so aTV Flash wins this round.
File transfer: This is where the big difference was for me. Using aTV Flash, I could FTP content across at speeds of 430kb/s (12 minutes to transfer a 45 minute show). But Boxee doesn't enable FTP. Unless you have sys admin skills, you HAVE to use SFTP - with speeds of 80kb/s (60 minutes to transfer a 45 minute show).
I have heaps of content that just sits on the Apple TV box, and it was obvious this would take weeks to get on there over SFTP. So after playing with Boxee for a while, and researching the FTP issue, I gave up and rolled back to aTV Flash. Obviously the $50 price difference wasn't an issue in June last year when I paid for it (there were no user friendly alternatives), and I got a year's worth of updates and support, but it may be an issue for you.
Obviously this is all the case as of 6 April 2009. The SFTP issue may have been resolved by the time you read this - but if this is a deal breaker for you too, maybe see if the Boxee community have responded to my suggestion on their discussion boards when making your decision.