In our dialog so far, we've covered a lot of ground. I read that you have a Wacom tablet, so I understand your enthusiasm for providing Wacom support. There should be a way to conditionally insert the embed tag. I don't know whether the HTTP User Agent request header reflects Wacom, but seems to me it should (if you have the browser plugin installed, hmm or is it an 'extension'? it might be mentioned in the UA string, along with Flash and/or Silverlight etc). If you can't autodetect, perhaps the app init() could display a confirm prompt "activate Wacom support?" and body.appendChild the [embed] or [object] Wacom object. This would preclude the chore of maintainng dual codebases.
The main problem with the Wacom plugin appears to be that it gives nasty error dialog for the users not having it installed.
To quote stewie:
The main problem with the Wacom plugin appears to be that it gives nasty error dialog for the users not having it installed.