Wow, you guys are really helpful. Thank you for the advice. I love Audioholics. My wife will feel differently I am sure. Here's what I am trying to do. Any input would be greatly appreciated!
Bluray/DVD/CD player
Likely either an Oppo or PS3. Easily accessible on top of the credenza the components will live in. Either work well, if you game its a no brainer
iPod/iPhone dock
Very optional but wife would love it. A USB connection might suffice.
Pioneer offers a great interface on their AVRs with no dock required, however if your networking, the dock may not be needed
Browse home network
Audio, images, non-BR movies from 4 Tb. RAID + Mac. If going with PS3 may use PS3MediaServer. If the receiver is networkable I may go with Oppo. Will also have 500Gb USB attached to whichever component for times when network is swamped. Trying to avoid buying a Mac mini.
The aforementioned WDTVL is a great interface with plenty of modded firmware available to suit all needs.
Stream external services
Netflix, youtube, hulu, etc. We don't have, nor will we get, cable. I plan to rip bought DVDs and Netflix rentals to remove advertising (for my daughter) and Blueray for the really good stuff.
Cant comment on ripping rented DVDs

See WDTVL for all other needs
Universal Remote
Probably RF as equipment will be in a credenza, only player will be exposed, but will consider IR if its worth it. A Harmony One or similar most likely.
Budget?
Video up sampling
I'm a bit on the fence here. Plenty of material won't be HD, just trying to get best possible image on a Sony 60" XBR. Would prefer to buy once here and live with it for 5-7 years before upgrading.
Your display will handle the upscaling
3D/HDMI 1.4a
I think it's lame but the TV comes with glasses and my wife and daughter will love it.
The tech is ever changing so dont get to hung up on it yet
Good audio
Have B&W 603 s3 towers now. Want to go all HDMI with good cables to the speakers, eventually upgrading to a 7.2 system.