differences between using wmode="transparent", "opaque", or "window" for an embedded object on a webpage
Here is some weak adobe documentation on different flash 9 wmode settings.
A note of caution on wmode transparent is here in the adobe bug trac.
And new for flash 10, are two new wmodes: gpu and direct. Please refer to Adobe Knowledge Base about wmode.
Opaque will cause less system strain since 'transparent' will still attempt to apply alpha. The reason you see transparent used instead is because most web authors don't pay attention to detail (ie, just copy-pasted some embed code they found).
BTW, you are correct about it being undocumented. The best I've ever seen is a blog by a guy who claims to have talked to a Macromedia developer about it. Unfortunaetly I can't find the link.
EDIT: I think it was this one: http://www.communitymx.com/content/article.cfm?cid=e5141
also, with wmode=opaque
and with IE, the Flash gets the keyboard events, but also the html page receives them, so it can't be use for something like embedding a flash game. Very annoying