Which RAM configuration is better, performance-wise:

DDR2 2Gb 800 MHz CL-4
or
DDR2 3Gb 800 MHz CL-5?

(Both would be running in single channel mode. OS = Windows 7, x86.)NOBODY can give a right ANSWER without some other factors.
Using applications that never reach 2 GB. Simple answer, GO with the faster.
But do you really have an application the just must have 3 GB to work in? Does it really use all the 3GB? Would the latency issue arise in that PROGRAM?

Even with more details, there would still be no clear answer. The latency issue is not as easy as you might thin k.
The only clear answer is that if everything else is equal, the lesser latency would be better. Maybe. If you want to compare two 2 GB modules, we might... or might not.
Read this very carefully.
http://en.wikipedia.org/wiki/CAS_latency

Now let me give a better answer. But I have to change the question.

Q. Is a 1 GB slow RAM going to work as good as a fast 2GB RAM?
A. No, the 2GB will perform better in most cases. It depends.

I see. Well, the applications in question are quite demanding, as typical of GRAPHIC games. E.g., TES-4 Oblivion tweaked to allow addressing more than 2 Gb memory.
Seeing as all hardware settings are intervowen, I guess I'll go for the higher cl & bigger size; otherwise, with both modules running at the same settings, there'll be either over- or underclocking of latency & voltage settings on one of them...
Unless there is some BIOS option to process the modules in a different way, separately (is that theoretically possible?), or, maybe, some utility for that?