When embedding Flash .SWFs in HTML, there are several choices you can make for the wmode parameter. I've always been a bit confused about which was which, so I set out to today to pull together as much information as possible on the subject. Here is a quick run down of the choices, and what they mean for your Flash .swf.
wmode=window : Usually the default option. This puts the Flash movie on top of all other content on the HTML page. This means Flash won't play well with other HTML elements, and it won't adhere to z-index ordering. In some cases, this mode will net you the best performance for your Flash game or application. This appears to be the safest option for getting your Flash to work properly in the majority of web browsers.
wmode=opaque : This mode is supposed to let Flash play well within an HTML page and adhere to z-index ordering. This option will disable hardware GPU rendering and default to software rendering. This mode is not recommended for use with mobile platforms displaying video. This mode also sometimes interferes with capturing keyboard events in Flash. At the same time, some game developers have found that opaque nets them smoother frame rates.
wmode=transparent : If the background of your Flash movie is transparent, the HTML page will show through. Just like opaque, this option is supposed to play well with other HTML elements and has it's uses in the arena. However, this option takes a significant amount of processing power to render the transparency. Like opaque, this option will automatically disable hardware GPU rendering and default to software rendering, is not is not recommended for use with mobile platforms displaying video and sometimes interferes with capturing keyboard events in Flash.
wmode=gpu : Uses the GPU for hardware accelerated rendering. This may sound like a good idea, but that is not always the case. Although running on the GPU can be very fast, in some cases loading and reloading graphics data to the GPU can be costly and time consuming. You need to test this with your apps and the target devices to make sure it is beneficial to performance.
wmode=direct : This mode bypasses the browser when rednering. This mode is required for Flash "StageVideo" to work in Flash player 10.2. This mode appears to not play well with some HTML elements (similar to wmode=window).
This is what I could find today. If you have any additions, subtractions, or updates to this, please tell use in the comments below.