I was having a hard time getting Flex Builder on my Mac to behave. I came across a post at Big Spaceship Labs that put me on the right path. I tried things, and came up with a reasonable solution, which I added as a comment to the original post.
This technique is useful for keeping several Flash Players on your system (or anything, really). I think I read that MultiSafari uses this trick. The trick is to change an application's bundle identifier. You may have noticed that Mac OSX seems to magically know about all the applications on your system, even though you didn't use an installer for most of them. It uses the bundle identifier (and I believe the bundle version) to keep track of them. I believe that Max OSX treats all applications with the same bundle identifier and version as the same. Internally, they probably form a composite key in a map. Furthermore, most associations (such as "Open With") are made to the bundle identifier, not the application's path. This is so that you can move an application to a new directory without breaking anything. It also means that, if you have 2 applications with the same bundle identifier and version, there is no way to choose which one will launch.
It's surprising how well the whole application list works on Mac OSX. I still had some problems in 10.4, but 10.5 seems to be rock solid in this area. And, when application developers know what they're doing, it works pretty well.