There are many, many builds of MAME these days, some of which claim to be optimised for certain chipsets or graphics cards. In my experience, you will only notice the difference when pushing the benchmark to the limit of the PC you're using - for example I use a Pentium-optimised build of MAME32, which on a like-for-like basis at the stretch of my PC (a high P4 with no additional graphics cards) can run polygonal or 3D-based games better than the standard counterpart.
However, since the MAME core re-write at 0.106 these other 'optimised' builds have become either redundant or less frequently supported as MAME now utilises graphics and sound hardware for emulation. In my opinion, stick with normal versions of MAME (ie. the command-line version as it runs much better) or if you must, the sort-of-official Windows GUI version MAME32 (or MAMEUI as it's now called) as it will make updates easier and is more commonly supported around the net.