If you do it in java, you can use your android phone or tablet as a remote. I have a remote app for my receiver (Pioneer SC-1222), but I don't have the receiver hooked up to my router...just because I am lazy.
About the HDMI issue, I see you can get HDMI/DVI out cards that will bitstream HD audio for $30 in case you need to get a new card.
http://www.tigerdirect.com/applications ... CatId=1558
Side note: I see you have the Elite series. I am jealous you have 12v out triggers and mine doesn't. I debated while the black friday deals were going on because the lack of a 12v trigger was pretty much a deal breaker for me. I tried to get the Onkyo 808, but they sold out before I could find out if their 12v triggers for zones 2 and 3 could be reconfigured for zone1. I settled with the 1222. Luckily I neither have my subs finished nor added a 240v circuit for my sub amp, so the 12v trigger is a non-issue for now. Later when I get that done, I will have to forever get in and out of the closet to switch the amp on/off if I can't come up with another solution.
Second side note: Why did they stop putting switched 120v outs on receivers? My old Pioneers VSX1014 has one and I could have used that with a transformer as my trigger if companies still put switched AC outs on receivers...