Okay. I\'m sick of this problem. This has to have an easy fix, I\'m sure of it!! I hope SO can help me to get rid of this once and for all!
The best approach is to use the Inclusion and Exclusion Patterns option in the Java Build Path.
For example if you want to exclude one project of being automatically build:
1- Go to its Properties->Java Build Path->Source.
2- Expand the folder in the "Source folders on the build path:" area
3- Select Exclude->Edit
4- In the exclusion patterns add **
Note: for more information on this patterns: Include and Exclusion Patterns