One of our readers claims that this isn't just related to Flash playback... it's possible that this lag problem is consistent across the system. Flash taxes your system more than most applications so it would show the lag problem more consistently than another application -- thus making it look like a problem only with Flash.
The suggestion at this point: cycle your wireless connection. By turning AirPort off and on again, some people are seeing the computer regain responsiveness. Obviously this isn't a permanent fix because the issue will most likely appear again after you reboot your machine... we can't say if the fix will persist for the entire session, either; the problem could come back before reboot.
Fellow TUAW blogger Joachim Bean suggests that the issues may be something related to PCI Express. Both the AirPort and graphics card are using PCI Express to communicate with the system. There's a possibility that the lines of communication are crossing during use. I'm still betting on a software issue -- at least, let's hope for that.
Let us know if this helps, or any other possible solutions you might have in the comments.