I run Flex Builder 3 on a mac and as my project grows - the compile time gets longer and longer and longer. I am using some SWC\'s and there is a fair amount of code but it
You want at least 4 gigs on your computer if possible, and make sure to override the default memory settings that eclipse/flexbuilder gives to the application.
If you're not sure how to do this, you can find the flexbuilder app in /Applications, right click and choose "Show Package Contents". Then go into the contents file and edit the eclipse.ini file. Edit that file have memory settings of at least:
-vmargs -Xms768m -Xmx768m -XX:PermSize=128m -XX:MaxPermSize=128m
It's also worthwhile to go into the eclipse/flexbuilder preferences and to check the "Show heap status" box under Windows->Preferences->General (This is in eclipse with the FB plugin, I'm assuming it's also there for standalone FB).
This shows the current memory in the lower right of the window and has a little trash icon so you can force garbage collection.
I'd also suggest turning off automatic building of the project when your files change (you can force a build with cmd-B).
We had a huge project with quite a few modules files and performance in FlexBuilder 3 was decent with these steps.