Do you mean 3DMark benchmark programs only? If so I would probably say '03. While it focuses heavily on the GPU, it does offer some system performance testing in the first test. And it also has CPU specific tests. Unfortunately the CPU tests have shown to be a bit buggy. It does offer comprehensive system comparisions, a nice feature but still has flaws. In fact I think Futuremark is currently not allowing detailed system comparisons. And the licensed version allows you to publish multiple projects while the free version allows only one.
I actually prefer '01 but it's fast becoming an outdated benchmark, and Futuremark has been talking about dropping the '01 ORB. Plus there really is no point in buying '01 as the licensed version is almost identical to the free one.
As far as '05 goes, I think it's a crappy benchmark.