Even if your TV has multiple HDMI inputs, most TVs can only output two-channel audio over the TOSLINK out (f'ing copyright protections). Therefore, to get DD5.1 or better you have to run the audio signal directly to the receiver via either HDMI or a TOSLINK. To get TrueHD, you have to run HDMI directly to the reciever.
If you're running audio to the receiver, it's a lot cleaner to run the video through too. That way you only have to run one cable to the TV (instead of one to the TV and one to the receiver for every device). That's why the HDMI video pass-through is important (and, in general, the more HDMI inputs on the receiver, the better).
Bear in mind that many recievers will not upscale component to HDMI, so you might have to run both a component video and HDMI cable to the TV if your source only has component out (e.g., a Wii or some STBs).
Now, if you're running the a/v to the receiver via HDMI to get DD5.1, TrueHD, etc., it's important that your receiver either (i) have the necessary decoders built in, or (ii) be able to process an LPCM (decoded) stream from a player with the necessary decoders.
In general, disc players (whether DVD, Blu-Ray, Playstation) are far more capable decoders (and you will find a lot more decoding variety). For this reason, it's best to have a receiver that will handle LPCM (i.e., a decoded audio stream), so that it can handle anything your player can decode (including future formats). That's the reason for the sticky at the top of the HTiB page.
As a side note, rather than have LPCM processing capability, you could also have analog inputs, but many devices like the PS3 don't have analog out, so your receiver better be able to handle LPCM via HDMI or have the necessary built-in decoders.
I'm no expert, but I think I have all this dialed in pretty well. Thoughts?