You went from one extreme to another...started with a crappy eMachine & now this? I thought you wanted a budget system? I agree with your decision to build (provided you find someone who knows what they're doing)...but personally, if I was gonna build a socket 939 Athlon 64 system, I would NOT get motherboard with AGP, I would NOT get a VIA based board, & I would NOT get a Jetway. If you're not gonna go all the way & build a system with PCI-e graphics (& I know you're not), ditch this idea altogether. Stick with a system similar to the one from CyberPower.
Consider these components...I've given you 2 alternatives (cheaper & more expensive) where possible:
Motherboard:
Socket 754 nForce3 250 w/AGP
http://www.newegg.com/Product/Product.asp?Item=N82E16813152043
http://www.newegg.com/Product/Product.asp?Item=N82E16813131512
CPU:
http://www.newegg.com/Product/Product.asp?Item=N82E16819104224
http://www.newegg.com/Product/Product.asp?Item=N82E16819103452
RAM:
You said you already have 512MB but you never said if it's PC2100, 2700, or 3200. The S754 doesn't support dual channel mode, so you "may" be able to just add 512MB to what you already have. But if you don't have PC3200, I suggest you buy 1GB (2 x 512MB)
http://www.newegg.com/Product/Product.asp?Item=N82E16820145026
http://www.newegg.com/Product/Product.asp?Item=N82E16820145440
Optical drive (DVD burner):
http://www.newegg.com/Product/Product.asp?Item=N82E16827130034
HDD:
If you wanna stick with PATA rather than SATA, CompUSA has a 160GB 7200RPM 8MB cache drive on sale this week for $40 after rebate(s)
Case/PSU:
$16 shipping kinda kills the deal. You might be better off shopping locally. Be aware that when buying a case w/PSU, the PSU may not be a very good one. Check the specs if you can, especially the amperage on the +12v rail. 16A is the minimum required, with 18A or better recommended.
http://www.newegg.com/Product/Product.asp?Item=N82E16811147011
http://www.newegg.com/Product/Product.asp?Item=N82E16811129140
Asus A7N8X-X
1800+ @ 8.5 x 200MHz
768MB PC3200 2.5-3-3-7
Asus A9550GE/TD 128MB
WinME/WinXP Pro