How much fan noise are we talking about?
Like can you hear it from a meter away?
yes, easily. and its not just the cpu or psu, its really both (tested using the FingerMark fan stopping system). i thought about swapping the cpu fan out with a zalman zm-op1, which i think would work even though its an 80mm and the stock is 70mm, but i never tried it. i think a more serious modder would have decent success by replacing both the cpu fan and the psu fan with zm-op1's. though the psu fan swap looks like it would a tad harder than any ATX psu fan swap due to the restricted space and pre-routed power cables going everywhere.
i had a p4 2.0 in there w/ onboard vga, so it was hardly taxing the thermal abilities of the system, but it would still get noticeably louder when just doing SETI@home for 10 minutes or so. the noise is pretty decent though, just air whooshing, but a die-hard SPCRer would not find it acceptable (i would not have it as my main rig in stock form).
edit: i should add that i love SFF systems, but if i was forced to use one as my main rig, i think the only acceptable one (in terms of quietness) would be a modified Zen. the others just have too many small fans. these fans can be quieted somewhat, but not made inaudible. i've played w/ the EZ65, EZ18, and biostar ideq 200V, so i haven't used them all, but from what i've read these are about the quietest anyway.