This topic is just up my alley..
1.OS:The best legacy OS to use is 98se or winME..
2.RAM:No matter what system board or CPU combo you are going to use you will be stuck with a MAX of 512MB of system ram because 98/98se/ME had stability issues with more then 512MB.
3.CPU:NO dual cores!!Single core only!!If the CPU has hyperthreading(p4) it will have to be shut off in the bios options otherwise you will have stability issues.
4.Motherboards:From my reasearch into maxing win me/98 the 2 highest CPU speed sockets will be intels 478 and 775 & highest FSB you will be able to go is 800FSB.The use of win98/me will be determined by the company that makes the board,go to the site that makes the board you are thinking of using and see if they have system drivers(Usb,Lan,Chipset,Audio) for me/98 ..if they do ya all set,it they dont that board wont work.
5.Graphics Slot
ci and agp only!!No pcie!!double check that the motherboards AGP slot is keyed to the card you are using..the keying determins the voltage the card will use
http://en.wikipedia.org/wiki/File:AGP_%26_AGP_Pro_Keying.svg
6.GPU:If using a nvidia video card the 6800xt is the last supported product with drivers..If using ATI video card the Radeon X850 is the last card with 98/ME drivers.Any card before the models ive listed will be fine..Just make sure to check the AGP slot keying.
7.Hard Drives:Any IDE will work no problem..but from what ive seen without using a PCI sata card most of onboard sata supplied motherboards dont have drivers for 98/ME.
8.OS Updates:If ya using 98/98se and you want to update the OS from microsoft update you will have problems if you dont have the mobo drivers on hand because youll have no lan to connect online.I fixed this issue by using an old pre 1998 lan card that windows 98se gave a driver to and i setup my connection from the internet setup option in control panel.But to get online to get the updates ya need to update to explorer 6.
9.USB:Usb KB and mice dont work too good with 98/ME when ya first installing the OS..make sure ya got adapters for ya usb stuff to serial ports untill ya get all the drivers in and then pull off the adapters plug in ya usb stuff.
10.Good Luck