Hardware problem: Overheating Clicking and Glitching

Hi. I have had this problem for a while, anytime I run some sort of game, it runs good for about 30 minutes, then problems show up. First, the computer tower makes weird noises, mostly like clicks, maybe it will do 1 click, then it just sounds different, maybe fans lowered speeds, then it makes another click, then another sound, maybe fans higher speeds. And this happens for about a minute or two, this is when the screen begins to glitch out. I get all kinds of problems, sometimes, everything will just freeze while those sounds go on, sometimes, my graphics go crazy, weird little boxes of colored lines. Then I just have to restart my computer. When I touched the tower, it was extremely hot, so I took it out, opened the side, and left it. Then I play the game again, 30 minutes all good, same shit happens, but the tower is not hot at all, its cool, cold. So I have no idea whats up. Any ideas?

The tower maybe cool; but the CPU may be hot.

Temperatures
Motherboard 42 °C (108 °F)
CPU 45 °C (113 °F)
GPU 53 °C (127 °F)
GPU Ambient 45 °C (113 °F)
IBM IC35L180AVV207-1 48 °C (118 °F)
WDC WD800JB-00FMA0 44 °C (111 °F)

And I'll run the game again and check the temps too.
EDIT: This is what it is when just running the game for about 2 minutes:
Temperatures
Motherboard 44 °C (111 °F)
CPU 54 °C (129 °F)
GPU 60 °C (140 °F)
GPU Ambient 48 °C (118 °F)
IBM IC35L180AVV207-1 48 °C (118 °F)
WDC WD800JB-00FMA0 44 °C (111 °F)

The hard drive temperatures are on the high side, but still in operating range. I would find a way to get the drive temperatures down, everything else looks normal.

I would suspect that your power supply is faulty. What brand supply do you have and what are its ratings?

JustPC(USA)
Model: atx-425-12v

And I just said screw it, and decided to play starcraft. Even a 1990 computer could fucking play starcraft but this piece of junk couldnt even handle it. When I rebooted, I checked the temps, CPU was 57 and GPU was like 65. C of course.. but I have no idea whats wrong.. this used to have a P4 processor until my dad took it to frys and they fucked it up with a "dual" core pentium fucking D processor and just fucked it up.

Sounds like junk.

The graphic glitches and lines before crashing is a common symptom of a failing power supply. The graphic card isn't receiving enough power on the 12v rail.

Replace it with a high quality power supply. Enermax and Seasonic are two companies that make excellent power supplies that you can find on store shelves. Antec, Corsair and PC Power & Cooling are a few companies that rebadge quality power supplies.

There are other good choices if you want to read up, you won't go wrong choosing any of the above.