To clarify further, the processor architectures should not be confused with operating systems, or application types. That is, just because Windows runs on x86 processors does not mean x86 Macs will run Windows software.
The operating system has to fit the architecture, and applications have to fit the operating system, and to a lesser extent, the architecture. A good deal of software deals altogether with the operating system, with no reference to the underlying architecture. In such a case, only the operating system really matters. Most Linux software works under this premise. Linux software will work under Linux, whether the Linux distribution is an x86, PPC, or other type.
With Mac software, it gets a bit more tricky. Apple has been asking people to recompile their code for x86 and PPC. This doesn't mean that the code actually made any reference to the architecture, but rather that it's best to cover one's bases. So, if we're talking Mac software, just download a Universal binary where possible (To optimize both architectures, as well as the fact that it will be the latest version), and whatever version is available where that's not possible.