What motherboard and PSU do you have? In fact, full system specs might prove helpful.
Most modern systems don't really use the 3.3V rail much, in older systems it was the source for CPU power. If it's running low it won't damage your board or components but anything that uses it might not have stable operation.
What's more significant is if the PSU's putting out unstable or low voltages it may be time to replace it before things really do go bad.
Low voltage typically won't damage anything, just under-power it causing it to not run appropriately. The main concern is that it is a sign that the power supply is failing to work correctly, and has the potential to spike voltages, which is a bigger concern. Run HWInfo (free) and have look at all of your voltages under light and heavy loads. Odds are you need to replace that PSU with a reputibly made unit asap.
Also, list ALL your hardware components and make/model/age of your current PSU
What motherboard and PSU do you have? >> I have an ASUS M5A97 LE R2.0 and the PSU is a TECH C3 DSAII 500VE .
Both with 9 years in use. By this time I am not sure the electrotic capacitors inside the PSU are still healty [ ? }.
So far I haven´t had problems with unstable operation. Personally I don´t think lower voltages can damage the mother board , but I decided to ask anyway .
I think you have the right idea. Your PSU brand is unfamiliar to me but 9 years is a long time for any but high quality capacitors to be in use. Another common problem component are resistors that shift value.
I'm not sure exactly what the 3.3V output is used for on that board but if the 3.3V rail is going bad it's not hard to imagine the 12V rail isn't long behind. Best start looking for a new PSU and change it before anything serious happens.