I think you need re-read the MS article about /PAE and /3G
http://support.microsoft.com/kb/283037for any 32bits application, it only have 4G of address space. So no matter how much physical memory (over 4G) you haev, it will only use up to 4G. But whether that 4G is physical memory or page file (which is hard drive), the application itself doesn't know (and doesn't care), OS handles it. If you have /3G turned on, the application can have up to 3G of stuff in actual physical memory, instead of page in and out using paging file.
Whether the /3G switch will benefit you or not, depends on the application. You mentioned it is running memory-intensive app, so it should, because by doing less page in and out, your performance should be better.