Recommendations for a Windows Media Centre substitute?

You should take a look at Moovida

I recommend XBMC (Ubuntu Install from PPA Instructions). It has options for a live-cd install, or can be installed as an application on Ubuntu. It is extremely configurable, but beautiful and functional out of the box. Of course, it has full LIRC support. It is skinnable, so can look like anything ranging from Windows Media Centre through to Apple's simplistic Front Row.

It supports "Series" information - put all your Grey's Anatomy episodes inside a "Grey's Anatomy" folder and tell XMBC that it's a TV show folder, XMBC will then scan the internet for information on the show, setting the folder up with a custom logo and cast information. Similarly for any movies you have digital copies of.

It also support VDPAU, which will give Nvidia card owners full hardware acceleration. This is crucial for boxes like the Acer Revo (Google product search), which features Nvidia's ION chipset - without VDPAU support, that device's Atom processor wouldn't be capable of 1080p output.

It doesn't integrate any form of live TV to my knowledge, so if you need to integrate your tv-tuner card, then you're better of with perhaps MythTV or Mythbuntu instead.

Why not Boxee? You can find it here, download is possible after registration, both 32 and 64 bit debs are available.

If you require TV checkout MythTV, if not XBMC. Depending on your hardware, you may decide that you want to avoid using a window manager entirely. You should probably do some research...