Well, the more bots you have the bigger the chance one well develop to do something useful. If you have a dual-core machine you can run two instances with 500 bots each connected with teleporters, to speed things up. I don't have dual-core on the machine where I'm running this sim, but the speed is still decent in the beginning, 4,5 cycles/sec. It will slow down once the bots have developed a lot of dna and start doing stuff. Also I use to put drifting shapes in at a later stage which will slow it down even further, but I'm the patient kind. It helps to have two computers for this stuff, so you can run it non-stop. Last time it took a couple of weeks before I got a good population of bots.
The heterotroph kind of sim I'm running on this computer, on the other hand, doesn't seem to do that well. I only got 100 bots left. I guess it needs more tweaking.