In addition to my experience that certain games (even Half-Life and GTA3) run faster in Win98 there are other compelling reasons for me to dual boot Win98/Win2k. One of those reasons is to run Norton Speed Disk on my drives in Win98. I know that the latest version of Speed Disk runs in Win2k and WinXP, but it runs slower than even diskeeper which is pretty slow. So I boot into Win98 and run Speed Disk which defragments my drives at least 3-4 times as fast as any program can in Win2k.
Another reason I like to keep Win98 around is because I like to have a barebones Win98 installation with only 2-3 absolutely necessary programs and minimal Windows components. This allows me to have an OS with a small registry and small easily defragmented installation particularly for games. It would be nice to game benchmark comparisons in both Oses to settle this issue once and for all. But as it stands, I feel my games run smoother and faster in Win98. All my work gets done better in the much more reliable Win2K environment.
Other reasons for dual-booting are just to have a backup OS in case something bad happens to you primary OS, so you can still do your work, and if neccessary to troubleshoot and manipulate files. Even though I'd prefer to use NTFS, this is why I still use FAT32 in addition to access in DOS. Maybe it is time to just move to Win2k/NTFS, but I haven't seen or felt anything conclusive about that, beyond certain people saying that one is of superior intellect if one boots only Win2k/WinXP.