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I'm usually not afraid to tear open a piece of electronics and attempt to troubleshoot and repair, but I don't really have that kind of time anymore. Hopefully someone will be able to offer some good advice.

I have a system where the VGA out is messed up. The Picture is really dark with a green hue on one side. S-Video out of the system works fine.

Important to note:
I have a second system that works perfectly with all the same cables and this is a new fault that just showed up.

I'm thinking it has something to do with the voltage the VGA box is drawing from the system. My VGA box has an LED that lights up when the system is active. On my system that works fine, that LED is bright, but it is dimmer on the faulty one. If I plug a VGA cable into the box connected to the faulty system the LED dims even more. If I unplug it it gets brighter. I have a second el cheapo VGA cable that works with the good system, and doesn't with the faulty one, so I'm pretty sure the fault is isolated to the system, not the VGA boxes. Any ideas?

The 5V line sounds like a likely culprit. Pretty much the only thing the VGA box does is apply capacitors to the RGB lines- and those caps are wired to the 5V line. The other thing you might check is the connection between the power supply and motherboard, because sometimes that connection will either get dirty or the contacts will be making a poor connection. I believe you can bend the contacts out a bit on the power supply, as well as clean the pins on the motherboard and that would take care of a connection issue.

I saw that PSU fix after a quick google search. I'll give it a try. I also just remembered that I have a modchip installed. If that somehow suddenly went bad, it might be causing issues since I believe that pulls power from the 5v line. The fact that S-video still works leads me to believe that something close to the AV out may have gone bad. There may be capacitor(s) on the 5V output that could be going bad.

One thing to try would be to put the power supply from the non-working unit into the working unit and see what happens- that should tell you if you're getting enough current on the 5V rail.