Sorry if this duplicates.
Test Drive - the first really somewhat sort of kind of accurate driving game.
Beachhead - the first game that anyone I know thinks was really good for a PC
Corel Draw - how the mighty have fallen. This was the first vector drawing program with real chutzpa and it came with scads of free-ish clip art.
Wordperfect - another fallen giant, this was the first word processor that had real formatting and usefulness. Today it's still better than Word. ;)
Pagestream - launched the Atari ST as a business platform and sold probably a half million machines. Still available and still powerful today! It blows software like Scribus out of the water but it's not open source. :(
EMACS - the text editor that is its own operating system.
Solitaire - c'mon, this program has been around for two decades and is STILL the most popular Windows program.
TCP/IP - do I really need to say it?
QNX - still possibly the most popular real-time operating system. I first used it on the Bionic Beavers in Ontario back in (IIRC) 1984.
Eye of the Beholder - the game that made both FPS and adventuring cool.
I know there are lot more. My memory is getting pretty old like the rest of me... there were some games on the C=64 that are still not being reproduced today, one of which I remember as being a game in which you built a robotic factory rig that would deliver a payload through a processing system and then produce an end product, and had hundreds of level variations - one of my favourites, cannot remember the name but nothing like it exists today that I have seen.