I'd need more details to give you a definite answer, but I know that many computer manufacturers use mATX boards, so you'd probably start by refining your search down to those types of boards. Other than that, my best advice is to make sure that you are purchasing the proper type of motherboard to go with his CPU/RAM. Choosing the same chipset or at least chipset family will probably make it unnecessary to reinstall the OS.
Just out of curiosity, is the computer still under warranty? If so it'd be simpler to get a warranty replacement.
the current system is, an intel pentium D 1.8GHz, 3gb ddr2 667mhz, 400gb hd, and mATX mobo.
Im changing the system to an AMD mATX mobo, amd athlon x2 6000+, 3gb ddr2 667mhz, plus im installing a 485 watt psu, it has a 160watt psu, so im just upgrading everything, and installing windows vista ultimate 64bit. I am upgrading to a different mATX board, but its still mATX
And yes board under warranty, except, my friend just wants to upgrade for games, he wants this to be his gaming computer, i can buy everything, i just need to know if the holes match up or if i need to buy a new case
Yes a uATX board will (should) line up just fine, with a noted exception below. I would be more worried about the power supply though. Most gateway micro case PSU's I've dealt with have unusual dimensions and fan placement. In other words, you may have a difficult time shoehorning a 500 W PSU in that thang.
I know that newegg has replacement power supplies specifically sized for that, but maybe not the wattage your looking for. Also they were not rated well at all.
I recently bought a micro case that I thought was stylish and inexpensive, but not cheap. I also got a thermaltake 400W to drop in there and it was a great match. Got both for around $50 shipped. Here's a link to the case.