What is really frustrating is when you find programs that are extremely useful and they become incompatible with new systems. This is especially an issue when doing work for the government.
Things that make ya go grrrrrrrrrrrrrrrrrrrrrrrrrrrrrr
If you're okay with running at a limited resolution, you might want to give VMware or Virtualbox a try.
You can set up any number of guest operating systems that run on whatever platform you chose (Windows8, Windows7, WinXP, Linux in 32 and 64 bit flavors). For relatively new operating systems (XP and newer) there are rudimentary 3d acceleration and USB passthrough features, so you can literally use it like a fully functional computer, all while running on whatever operating system you want.
Windows 98 will install on a virtual machine, but you'll be limited to 800x600 resolution since there will be no video drivers, and there is no USB support. You can however mount floppies of varying sizes and capacities if you copy the data off of them ahead of time and it's on your hard disk.
But it would let you run a Windows XP VM, and a Windows 98 VM, and then for the really old stuff, you can install DOS and windows 3.1 on a virtual machine as well (although I'm not sure what the status of network drivers is if you need network capabilities).
It's worthless for games because you don't get MIDI and some of the bells and whistles like 3d acceleration, but for productivity applications that need to run on an older OS, it's
really convenient.
Zip drives and 3.5" floppy drives are readily available in USB. For 5.25 it's going to be harder, but there are USB controllers for them if you wanted to do some DiY.