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
I don't use Flex Builder, but I use the Flex SDK compiler everyday and I was wasting tons of time waiting for the MXMLC compiler to do its job until I found Flex Compiler SHell:
http://blog.zarate.tv/2008/12/07/theres-something-called-flex-compiler-shell/
Although in theory Flex Builder already uses this optimizations, might be worth checking.
As Clement said, use the HellFire Compiler Daemon. If you have multiple modules and more CPU cores on your machine it can compile them in parallel. Another option is to use IntelliJ (the commercial version) which offers the same feature.