More chips means less OC possibilities.
128MB DIMMs are usually 16 chip things - 64MB DIMMs are 8 or 16 chips.
If they are two 8-chip 64MB DIMMs and the 128MB DIMM is a 16-chip DIMM, it wont make any real difference if they are both the same spec.
However it is better to have 1 256MB DIMM than 2 128MB DIMMs.
With older memory types (EDO, fast page etc) there was a definite engineering reason to use symmetric pairs of memory banks. With this setup, the memory would be mapped in an interleaved manner, so that accessing all addresses in order would alternate fetches between the two banks. This reduced the time spent waiting for refresh cycles to occur (one bank refreshes, while the other is accessed).
I haven't seen anything definitive about SDRAM, and modern chipsets doing interleaving, but I have noticed that in many cases, a single DIMM contains 2 banks anyway. So I don't believe you need pairs of DIMMS for performance reasons (someone please correct me if this is wrong).
For overclockers, the current wisdom is that if you are having memory stability problems, remove one DIMM, and see if it helps. It may be that when using pairs, running them out of spec (overclocked) causes more timing problems.
Anyway, I'd get the 128, mostly so that you are only using one slot.
Free advice, and worth every penny.