I think the SR-4002 is likely a very good receiver, and should do just about anything audiowise you would need it too. The RX-V663 doesn't have a huge advantage with video or audio processing as I would only use the decoding inside a Blu-ray player to get my HD audio anyway (the Blu-ray secondary audio tracks only work when the Blu-ray player handles the decoding). The audio sent from the Blu-ray player is pure uncompressed multichannel PCM, meaning there is no loss of sound quality, in fact it should sound exactly the same as having the receiver decode from the HD audio bitstream (Dolby True HD, DTS-HD, Dolby Digital Plus).
The Onkyo should be dropped from the running period, it's l ikely under the power bracket of the Marantz and Yamaha receivers, has heat issues, has reported popping issues, and a few other beefs such as quality audio production (which may or may not be a real problem and it could just be in people's heads).
All that said, the Yamaha has a slight advantage in features over the Marantz. Those features may never be used though (such as HDMI 1.3 features). Neither receiver has a phono input, so an external phono preamp (which is generally prefered) would be needed for LP playback. Both receivers have preouts for all channels, so using the Marantz or Yamaha as a preamp with power amplifiers is an option. This is not so with the Onkyo.