I personally use jRiver MC16 and it does have uPnP server built in and the price is right.
For media players for the rooms I use old xbox's running XBMC
For remote control I use PlugPlayer that is available for both Android and iOS on my ipod touch. It allows you to select the media servers and players along with media with coverart, search, and transport control and it's cheap
To prevent the kids from watching movies on the xbmc do not add your NAS to the video sources and use plugplayer to initiate playback!
Eventually I will replace the xboxes with ATV2 running XBMC to support HD playback
For regular TV I use an HDPVR and an HD box hooked up to a monoprice 4x4 HDMI Matrix and run HDMI cables to my TV's
These are controlled by 3 Logitech 890Pro remote controls one for each room with the RF extender located in the equipment cabinet.