Win9x makes sense if you are not dual booting and want to drop to real mode dos Something you can't do in w2k due to its NT origins.
One of my 486dx2/66s runs OS/2 v3 on 8megs of ram which is totally silly but no other OS seemed to like the hdd in that machine at all. Nice thing is you can boot different dos disks on it's desktop without rebooting.
Good for you. Some folk here use removable drive bays. You can skip two of those by just using the Win98 cf card though, trim it up a bit to get rid of a lot of the IE crappola. It'll run a lot of win 3.x, win9x and dos software.
Having every machine with a purely MS OS is rather tiresome though. I like variety on my old kit. It's a hobby after all.