I have a multiple monitor setup and I enjoy watching shows in the full screen format. The problem is that even if I click on a different window for the sake of multi-tasking it closes the full screen window. Is there a work-around for this? Thanks.

I have that same problem and I understand how it's annoying but currently Flash does not allow any work around since the fullscreen functionality is built into Flash as is, with no configurable variables. I would suggest trying Boxee to watch our videos on the 2nd monitor since that program sort of always stays in fullscreen mode. I haven't really tried it much and don't know how well the program will run while it's not in focused view but you can read more about it here:
http://www.crunchyroll.com/forumtopic-576238/watch-anime-and-drama-on-your-tv-with-boxee/

do you know if there are any plans to add CR shows to the Windows Media Center lineup? I'm not even sure how that could be implemented without having a dedicated section like Netflix does since you'd need to take into account paid subscriptions.

and gah...doesn't seem to support 64-bit W7.

Hulu has found a nice work around for this on their flash player, http://www.hulu.com/watch/92766/dawn-of-the-dead. Go there for example and you'll notice on the side of their flash player an option called "pop out", at which point it opens a window with nothing but the flash player in it and then you can maximize the actual browser windows instead of using a flash based full screen. Right below that is the lower lights feature which is what I used before I noticed the pop out feature. I've really been hoping features like these will be put into crunchyrolls flash player for awhile, since for such a large and well organized site your flash player is relativity bad.

Someone has made a workaround for this. http://my.opera.com/d.i.z./blog/2009/04/22/watch-fullscreen-flash-while-working-on-another-screen. Basically he went and edited the dll of Flash to get it to work. Tip: the file to swap with should be located in C:\Windows\system32\Macromed\Flash\ or C:\Windows\SysWOW64\Macromed\Flash\ for Windows 7 64-bit for firefox. If you use Opera it's in the program folder. Not sure about any other browser. Not guaranteeing anything and it might only work for windows. Best of all it works on non-CR sites too.