If you mean the official fan test for the 40GB Version, I don't think that it's harmful for the PS3. But what I've heard about the fan test on the 60GB Version is that it's not really good for the components and that it could damage your PS3. I would say it's not worth to try it unless you've got a real reason for performing it.
That is what I tried to explain. There is no real fan test for the 60GB Version. It works for the 40GB Version and for the 60GB there's only a strange solution (something like turning it) which could damage it.