Not a PC one, but still:
Montezuma's Revenge for the Atari. One of the earliest games I remember playing, and one of the few times my dad sat down with me to actually play a game. Quality father-son bonding time (and I was like 3 years old at the time).
As for PC software...
Castle of the Winds (I remember trying to play this one when we got our first PC back in the early 90s. I had no fucking idea how to play it, I barely knew english. Still had a bit of fun by randomly doing stuff)
Microsoft Scandisk (I'm sure the "automatically fix every error it finds" option ended up deleting a crucial part of my Windows 3.11 install. After running it after a fatal crash, I was unable to enter Windows - actually, DOS told me the "Win" command was invalid! :O)
MusicMatch Jukebox (I started using this before the famous logo/UI redesign that everybody remembers -the silver/blue one- and I kinda preferred it to Winamp for a while. I remember seeing this skin, but I don't remember if this was the default or not.)
MSN Explorer (I remember using this one when I went to a cyber-café (remember those?) to connect to the internet, back when we only had Dial-Up at home and was incredibly expensive. Good times.)
Titus the Fox (fucking shitty game, to be honest. Then again, hindsight is 20/20 and I liked it back then.
Cool music too, even if kinda repetitive and grating after a while.)