I was having the same problem with my Illustrator and Photoshop plug-ins with the latest CS3 suite. I began compiling a list of what Plug-ins we’ve purchased and what didn’t work anymore. Then I started contacting vendors.
Several of them said they were working on new versions and would be ready for AE when it comes in July. For the time being, what you need to do is go to the FInder and get info on the application. There is a little check box that says run in Rosetta. Click this and 90% of the time you should see all your old plug-ins.
The problem with this though is your not running the application in the Universal Binary mode and not fully taking advantage of the processor(s).
As for the AE plug-ins I’ve contacted:
Peder Norrby has on the cow posts, that he should be ready when CS3 ships or possibly later in May.
Zaxwerks says they will be ready with ProAnimator by July and the update will be free.
Nucleo users will have many of the features in the standard edition built into AE so you might want to upgrade to Pro version when it comes out for added workflow improvements. This will be ready by July as well.
Hope this helps anybody