I've created a new set of threads for Windows and Linux each to separate the compilation guide questions, since the two build systems are so vastly different, and have completely different dependencies and troubleshooting techniques. Please refer to the following links from now on for compilation information and support:
Windows: http://forums.pcsx2.net/thread-11179.html
Linux: http://forums.pcsx2.net/thread-11177.html
Windows: http://forums.pcsx2.net/thread-11179.html
Linux: http://forums.pcsx2.net/thread-11177.html
Jake Stine (Air) - Programmer - PCSX2 Dev Team