I find a lot of the PC games in the late 80s and throughout the 90s were more innovative than the games today.
Here are some I really loved:
Planet's Edge - This game was like a mix of RPG and a space sim. You go from planet to planet doing things and the best part was you can reconstruct your ship however you want it. Also build your own armor and weapons. I also liked the fact that you can kill anyone in the game, the princess you're supposed to save, yeah just kill her....but it makes the game unbeatable though.
Circuit's Edge - This is a game based on a novel, so you know the story is awesome and it's extremely well-written. It's a first-person game where you are a guy going around town looking for a job. The atmosphere is excellent, it's cyber-punk obviously and this is one of the best cyber-punk games out there.
The Summoning - This is pretty much a Diablo game, before Diablo existed of course. I'm sure there are tons of games like this but this caught my attention because it's so well-done. It's a dungeon crawler, but the unique thing here is that there are towns within the Dungeon itself, which I thought was pretty unique. Also, this game penalizes you for carrying too many things, you will be overwhelmed by the weight of what you carry and slow to a crawl. Also, you can forget spells in this game after you learn them, which is pretty realistic if you ask me. But yeah, it's one of the best dungeon crawlers out there. A lot of the weapons and armor look badass if you ask me, which is quite an achievement for a game made in 1993.
Robinson's Requiem - This game is hard as hell, I can never go beyond a certain point. You can die from just about anything in this game. A cut on your arm and become infections, you can get a fever by sleeping in a cold area, you can get frostbite, you can all kinds of infections, you can die by losing consciousness, losing blood, eating rotten meat, eating poisonous stuff, eaten by a predator....it goes on and on. But it's worth a try.