The fans are probably defective and need to be replaced. And wasn't that a water cooled unit anyway?
In any case, given the age of that system, your only hope of getting official Apple parts is if you live in California, and even then it may have passed into the obsolete category. So you may have to scrounge ebay for something.
I will also say that programs like smcFanControl are a VERY bad idea. They tend to tinker with things that shouldn't be tinkered with. It can lead to false-positive diagnoses for one, and cause a lot of wasted time chasing down a phantom problem.
Just imagine a situation where you have a problem with say kernel panics. You bring your system to me, I run a diagnostic, and oh look, you've raised the floor on the fan speed values, so the diagnostic flags that as a failed fan because it doesn't reach the minimum speed in sufficient time. So I replace the fan, send you on your merry way, but the problem isn't resolved. You bring the system back, I run diagnostics again, see that the replacement fan appears to be having problems as well. While uncommon, this sort of thing can happen, so I throw in another fan, and send you on your merry way. I should also mention that it's a minimum of 2 days for me to diagnose the problem, get a new fan from Apple, put it in, and get it back to you. So, at this point we've wasted pretty much 5 days. You bring it back a third time, and now I get suspicious and start poking around, because that many fans failing in exactly the same way is highly unlikely. Eventually I come across the fact that you have smcFanControl installed, so I get rid of it, reset the SMC, and run diagnostics again. Now I likely find the actual problem after about a full week of chasing phantom problems, because this more detailed examination takes more time, and I miss the cutoff point for getting a part in the next day from Apple.
Now if you went and changed some configuration file manually, eventually I'll boot your system with an external HDD, see that the problem goes away, and then give you your system back saying you've got a corrupted OS.
And I'm one of the better techs out there. If I replace a part more than twice, I'm going to get suspicious. You take it to an Apple store, where they don't have to pay labor reimbursements, they may just keep throwing fans at it until the end of time. Apple doesn't hire people based on technical skill, they hire based more on personality. Many of them probably would never even think to go looking for something like smcFanControl, partly because they have no idea it exists.
Avoid those programs, or at least be sure to mention that you have them installed if you ever take your system in.
I recently was given an old 2x1.8Ghz PPC G5 in order to build a personnal server but I have troubleshooting with CPU's temps that are really too hot (75?C with no app open, only Finder).
I know these temps are not that "hot" but I can't imagine what it would be when I'll open Safari, iGetter, iTunes, CyberDuck, Adium and Photoshop CS4...).
I first unmount everything, blown inside some bottled air to make sure there were no dust creating overheating inside and remount everything.
Installed Leopard (last OS installable on PPC machines), made the last updates possible and restart.
Everything is working well althought this CPU's temp is so damn high and fans's speed are still at 300rpm. I was looking for some app that would do the same as SmcFanControl for Intel based Macs but for PPC's ones.
After many internet searches on many forums I finally admitted there were no software able to set fans's speed, the only way was manually editing the AppleFan.kext integer's values.
WhatI did, reducing the integer values to lower rates (256x multiples), then restarted the Mac but nothing happens. As I check the changed values, they indeed are the ones I edited but the fans still are at 300 rpm and the CPU's temp 75?C...
Does somebody have any solution for that issue, I feel I checked everything that was possible but nothing seems to work.
Any help is welcome...