350 watt is low for a PSU running load, which means you'll wear it down. But that depends on the quality of the PSU and the number of fans.
Fans are not that expensive and if they break it's not a catastrophe. PSU's are another matter.
You could run fans independently, keep the intake and HDD ones running fully as well as the exhaust ones, these don't have sensors and their speeds could be tied through SpeedFan at most with HDD temps to keep them useful, but that's not really useful overall. HDD's don't heat up based on CPU load, ytou could potentially run high IO load applications while the CPU speeds and its temps remain low, thus not triggering the speeds for these HDD fans.
While the CPU and other fans you can keep at variable speeds. The CPU has sensors, that's why you can adjust speeds based on load, which in turn will help you in several ways. Noise will be reduced to only when needed, dust on and wear of CPU fans will be reduced and keeping CPU at a stable temp, not necessarily the lowest temp is healthier. This means a delta temp between idle and load at the lowest possible.
This can be achieved by keeping the CPU under low fan speeds when idling, and at load at high fan speeds, so as the average temp isn't offset too much. This will help interconnects of CPU and other parts not strain themselves from thermal expansion and contraction from the large temperature difference, as opposed to running just one speed and having a large delta temp.
Noisy, sucks more dirty air through the case over the computer's lifetime. – Fiasco Labs – 2014-05-11T04:25:39.120
@FiascoLabs What if I clean the case out? And I don't care about noise. – Jon – 2014-05-11T04:26:55.453
1It's not a case of cleaning the case out, you just are drawing more dust laden air through the system. There are several cases out there with positive air pressure cooling that have air inlet filtration to prevent this. This is opposed to the negative pressure cooling currently used on most systems where you have the fans expelling the air instead of pulling it in and blowing it through the case. It's easier to filter with positive pressure systems. – Fiasco Labs – 2014-05-11T04:33:45.393