The biggest culprit was the cd-rom drivers and the mouse driver.
Our PC “only” had 4mb of RAM which was the minimum for Doom, but exiting Windows into DOS after boot left a lot of cruft in memory.
The first time I tried starting the computer and bypassing autoexec.bat (which I learned from reading on a BBS) I was scared it was going to be permanent. Luckily it wasn’t.
All I can think about was trying to muck with IRQ conflicts or messed up awful windows 95 drivers later on to get my game working. I'm not sure I miss either of those much but I also switched to Windows NT early and kept an old decked out Pentium 1 for dos games that ntvdm wouldn't play nice with.
Nodding though, oh man that got me into developing things like you wouldn't believe.
Quake 1, 2 had a huge community around coding or map making. Tribes 2 was absolutely all about mods. Command and Conquer with it's rules.ini or StarCraft with its gui scripting stored in map files I spent so many hours messing with. It was all about making something crazy to show off when you went back to school or later to a lan party to wow everyone.
I still wonder how we managed to do that just by reading books or manuals and sharing info with friends.