change the motherboard, cpu and HDD. maybe a case that isn't too bling I'll leave this to you as its a matter of tastes.
E4400?
Well go with anything with a p35 chipset however with a $40.00 rebate this is hard to go past
http://www.newegg.com/Product/Produc...82E16813127031
500gig
http://www.newegg.com/Product/Produc...82E16822144450
(I'd prefer the samsung spinpoints as they're very quiet but they're like $30 mor)e
ddr2 ram is what you need preferably 800 speed but 667 is ok.
http://www.newegg.com/Product/Produc...82E16820231098
Everything else can pretty much stay
EDIT: this looks like good value
I'm a bit sleepy and can't do any maths to total it all up ATM but if possible and it fits within your budget have a shot at this instead of the e4400
http://www.newegg.com/Product/Produc...82E16819115005