There are a number of options for a C2D rig that supports Win98se. It mostly comes down to motherboard and chipset. Newer chipsets no longer support Win98se, so you'll have to pin down a more "vintage" chipset, on a mobo that also has C2D support.
Check out
this thread. Also
this thread.
I also run a multi-boot setup, with Win98se, W2K, and WinXP. That is the primary reason why I choset the Conroe865PE mobo to upgrade my main rig - to keep Win98se compatibility.
The availability of that mobo is slim (I had to import them from Germany, the .au dealers were out of them). You would likely be better served by that Gigabyte micro-ATX board mentioned in the above thread, revision 2.0 supports C2D, and NewEgg.com carries that mobo, unlike the Conroe865PE. (
link)
The good news is that this "older" mobo also benchmarks rather well, see the near-to-last post by me, linking to a benchmarking thread.
Another, perhaps easier (more available) option, is the Via-based ASRock 4CoreDual-Vista board. (
link) Via's Hyperion drivers and USB drivers still support Win98se as well. (I prefer the 865 chipset stability-wise to Via, though.)
Edit: Win98se also does not support HDs bigger than 128GiB. (No 48-bit LBA support in MS IDE drivers.) I get around this issue using a Promise Ultra133 TX2 PCI IDE controller, which has a BIOS and drivers that support 48-bit LBA, and work in Win98se, W2K, and WinXP/2003. The best drivers are the ones available from Maxtor's site, they sell a rebadged version of that controller card.
I'm in the process of using Ghost 2003 to transfer the partitions from my old main rig (the KT400 XP1800+ rig) to my new main rig, a Conroe865PE E4400 rig, along with transferring my Promise controller card, since the HDs are effectively tied to that card. (Bought another card just in case too.)