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 always disable "automatic compile" for Flex. It compiles too much, takes too long, and so interrupts my work.
If you have many different project files and all of those needs to be recompiled, but you also have other projects open and don't want to close them always you're doing a build, you can also use Eclipse Working Sets.
Unfortunately, the default Flex Navigator does not support working sets. But you can open the Package Explorer with Window / Show View / .... Click on the little white downward arrow to the topright and select Top Level Elements: Working Sets. You can then add Working Sets (aka groups of projects). Each project needs to be in at least one working set ("Other Projects" being the default), but can be in several.
Now with Project / Build Working Set / ... you can instruct Eclipse to build all the projects in this working set, but none of the others. This is especially useful if you suspect your project references to be sometimes broken - otherwise building the 'topmost' project should trigger subsequent builds automatically.