Macs until this January ran on PowerPC CPUs, but the switch is on to bring them all into the "Intel inside" world. Apple realized this transition would be very hard for software vendors who would have to recode their products for the new CPUs so they basically bought a company called Transitive for its translation technology, which Apple calls Rosetta.
Under Rosetta PowerPC code is translated to Intel code. This means there is considerable overhead on startup and when new code is needed by the application during use, but it's much faster than emulation which is basically a virtual hardware machine made out of software within the OS - pretty technical, and not fast.
Anyway what you need to know is that PowerPC programs, the vast majority of them, run just fine under Rosetta, but at somewhat of a performance penalty. In something like a text editor this would be almost undetectable, but in a 3D FPS it could really drag down frame rates and overall performance.
The answer is Universal Binaries: programs that are compiled to run natively on both Intel and PowerPC. More and more are released every day. UT2004 patch 3369-3 (I believe it is) is a good example; it's over 100MBs but contains code for both PowerPC and Intel Macs, making the game "hardware agnostic" and giving you great performance on either CPU.
Hope this explains it.