The 40GB has no SACD support and has no Playstation 2 backwards compatibility. Not sure if that matters to you, but something to keep in mind.
They sell separate Sony remotes, like the one here:
[ame=http://www.amazon.com/Sony-PlayStation-Blu-ray-Disc-Remote/dp/B000M17AVO]Amazon.com: Sony PlayStation 3 Blu-ray Disc Remote: Video Games[/ame]
The system has bluetooth, but has no IR receiver, so Harmony remotes will probably not work. I heard there are USB IR receivers you can add FWIW.
As a media center, you can basically stream media content (music, pictures, videos) through your network to the PS3. Last I heard, I think DivX support was coming to the PS3, not sure where it stands now...