If your goal is to reach 4GB then no - it doesn't really matter.
4x 1GB will probably work out slightly cheaper at the moment, however it does mean any future upgrades will require you to remove modules.
Saying that, 4GB should be fine for a long time and even if you do require more then you'll probably be looking at DDR3 in the future and that requires all new memory anyway.
If your heavily into overclocking then the lower number of physical modules the better (so I'm told) is the way forward.
You can then keep the memory specification a lot tighter.
According to the "Vista Experience" my memory rating took a bit of a nose-dive when I first moved from 2GB to 4GB on my 965 based motherboard (4x Geil 1GB).
Subsequently I moved to a P35 based motherboard with 4x Crucial Ballistix 1GB and the memory rating rocketed - this may indicate the 965 chipset isn't as happy with 4 modules as the newer P35.