You're not alone. I would like to know such things as well.
Here are just some thoughts from the top of my head in no particular order:
Win9x was relevant from 1995 to about 2004ish (when XP SP2 was released). Good thing is to limit books/articles released in that time period.
IDA Pro is a nice tool (a must?) to have while dealing with Win9x.
@rloew might give some ideas as well.
Try looking in old articles from The Wayback Archive.
Look inside Win9x disks content, there might be references to some books (tours/guides/cd sampler thingies alike).
Download and have a look inside the SDKs.
I know that Visual Studio 2005 is last version to compile Win98 compatible stuff. (even if you have to compile apps inside WinXP)
Learn about the limitations (limited API calls, Unicode support)
Driver architecture (VXD, PDR, MPD) is unique to Win9x, so it's hard to make drivers, since you cannot use knowledge from other OSes.
I would like for someone to dive deep into NTKERN.VXD - expand it so the NT compatibility is much greater, if even possible.
Don't get your hopes high for writing ground-breaking drivers, Nouveau for Linux is made for decades and is not perfect. Maybe basic stuff like an universal better IDE driver to replace the Microsoft's default one, or an universal HD Audio driver is possible. But something like GPU drivers? Probably impossible.
Keep in mind that a lot of the Win9x kernel is still 16-bit and even DOS based, making it even harder to improve it!