I have a very strange problem. I am suddenly having problems with MB, CPU, and GPU temperatures. I built my current computer about 2-3 months ago. I am using an ASUS P5N-D MB with an Intel Q6600 quad core, and an XFX 8800 GTS Extreme graphics card. After building this rig, my idle temps were about mid-30's for mb, high 30's to low 40's for cpu, and 45-50 for the graphics card (according to nvidia control panel).
Now, suddenly, my CPU is idling at about 50 C, MB at low 50's, and graphics card at high 50's to low 60's. My cooling consists of a front 120mm fan sucking in, a rear 120mm fan blowing out the back, stock CPU fan, side 90mm fan sucking in at about mid point in the case. Also have stock cooling for the graphics card, and the PSU has an intake and exhaust fan.
First I checked the mounted stock fan on the CPU, as I had problems getting it on when I set it up originally. It's still seated nice and tight, and not much dust in the heat sink fins. My 3 case fans are all running fine as well. I blew dust out of everything to make sure there was no restrictions, but there wasn't a whole lot of dust yet. Took the cover off of the graphics card and there was alot of dust in it between the heat sink fins and the fan. Cleared it all out and put it back together, but this made absolutely no difference. I have verified the GPU fan is in fact running. So basically, nothing, including fan speeds, has changed, yet everything is getting hot all of a sudden. I've even taken the liberty of making my graphics card fan run at 100% all of the time, and still no difference.
I'm kind of at a loss for troubleshooting this. I'd like to avoid buying more parts if I can, since the symptoms tell me something has changed to restrict airflow somehow.
To check if airflow in/out of the case is the issue, run your system with the side panel off. If that drops temps more than a few degrees, you've got a case airflow problem.
Also, you didn't mention checking whether or not the PSU fans are still working properly.