This'll probably be no news to many people, but it's worth repeating:

First, you want to recompile the source code, because almost no-one wants to re-write a program using a hex editor. Change some values, sure. Re-write? Nope.

Second, the source code is likely lost, so you use a decompiler.

Third, the decompiler probably won't be near an exact match for whatever compiler was used, so you're going to get a fair amount of raw dump, at best.

Fourth, you now have to understand this mess.

Fifth, you need to re-write it to run on XP, Vista and Win7.

If you have any sanity left, it's probably three to six months later - For one game.

Much easier to throw it in an emulator. Unfortunately, there's no "Windows 95/98 emulator" you can just download and run on your computer. You can run it in a virtual machine, but that would require a legal copy of Windows 95/98.

There are programs like Wine, but they come with their own problems - Plus, they try to emulate the latest version of the OS, not ones popular about a decade and a half ago.

So, we get stuff in DOSBox or other wrappers because one game a week in DOSBox is still much better than one game every three-to-six months that runs natively.