Identifying program that make use of multiple cores

Edit - "programs" - sorry

I'd appreciate some advice from those-in-the-know. I know that multiple cores are good, but I don't really understand what they are for...

We're looking at replacing a dead G5 with a Mac Pro. I know that there is supposed to be an update coming, but I don't know if we can put off the purchase much longer. Regardless, our biggest debate at the moment is whether it is worth paying for the extra cores or not (currently the single quad care vs 2 quad cores). As I understand it, only certain kinds of programs make efficient use of multiple cores, and therefore the extra processor may or may not make a difference for us.

These are the programs that we are interested in (I'm sure some here will recognize them, but I'll give a brief description in case it helps those who don't):

FlowJo - for analyzing very large data sets (>1x10^6 events/file) for flow cytometery. Each event containing multiple parameters. Renders the output in different graphical formats. I tried contacting the developers and they said, predictably, "more processors good! more RAM good! Big computer good!". Not as helpful as I'd hoped.

Amnis - similar to flowjo, but also includes individual images for each event. This will have to be run on Windows via Bootcamp.

Volocity - for analyzing 3D imaging data (well, 4D since it's also done over time). Reconstructs structures in 3D from "stacks" of 2D images, creating "frames". Multiple stacks over time = movie. Identifies objects in the frames and then follows their movements over time.

Genespring - for analysis of large sets of gene expression data. Compares between multiple sets. Performs a lot of stats.

I don't know if you can identify what sorts of programs benefit from more cores (I can't, obviously). I suppose that for some, more RAM may make a bigger difference than more cores. We'd like this machine to last a number of years, so we'd like to get this balance right. I know that waiting for the update would really help.

Thanks. I really appreciate the advice.