Definitely agree with your choice for the Thief games! I tend to replay those games every few years lol. Only recently got Vampire: The Masquerade - Bloodlines and I've really enjoyed it, I just need to finish it. I've yet to really spend much time with System Shock 1 and 2, but when I next crave some cyberpunk, I'll definitely get onto it.
Off the top of my head, my picks would be:
Good Old Games today:
1. Broken Sword 1, 2, 3
Always wanted to play these when I was younger at my friend's house but they never wanted to boot them up because they were difficult. I bought them myself and then bought them again more recently on GOG, and my opinion of these games, specifically the first three, is that they're such enjoyable, light, humorous little adventures. Really comfortable to play on a quiet afternoon in with a cup of coffee. I share this view for quite a lot of classic point and click games honestly, but Broken Sword is a favourite of mine.
2. Deus Ex
Holds up brilliantly. I used to play this and replay this a lot as a kid, and few games scratched that cyberpunk itch for me the way Deus Ex did. Although some of the voice acting is a bit wonky, overall the game is so exciting. Plenty of different ways to play each level, multiple ways of upgrading your character, an exciting (albeit ridiculous, but kind of the point) story, and I'm a sucker for that late 90s/early 00s angular polygonal graphic style. It just feels so industrial, which really fits with a game like Deus Ex.
3. Planescape: Torment
I don't mean to be contrarian, OP, I really don't! I respect what you said about this game because it definitely leaves up a lot to reading. I found that quite refreshing though. Combat wasn't the key aspect to the game. I recently finished this game and I'd consider it a new personal favourite of mine. The art style is gorgeous, the storylines and how they branch off are beautifully structured, the ways you can organise your party, the combat, the side-missions, the looting, the different ways you can do certain missions, and even areas/lore that you can completely miss on a first playthrough. Maybe I'm crazy, but I actually really enjoyed drawing out a map for the modron maze too lol. Really loved this game, I never had the chance to play it when I was younger but I feel it must hold up rather well if a new player to it such as myself can get to grips with it.
Shoutout to Heroes of Might & Magic III which I was close to putting in this section. Love that game too! I'd also like to show my respect to the Myst franchise which just feels truly timeless.
Games that haven't aged so well:
1. Hitman: Codename 47
I was really looking forward to playing this as I love the Hitman series, and this one was only available on PC (the other games have been ported to console numerous times). While I like certain aspects of it (managing your money/resources for each mission, some missions restricted to a time limit - I feel this definitely adds to the tension the game is aiming for), I felt it just wasn't very fun to play. The controls felt awkward and whenever you died, the level doesn't quite restart fully. It's more like that Agent 47 is restarted, but your progress/damage done is still apparent as the enemies might still be shooting at you. It just felt like a headache to me.
2. Silent Hill 4: The Room
I bought this recently on GOG but I also played it not too long ago on my PS2, and this game feels like the turning point for when the Silent Hill series was going sour. It's not necessarily bad, and it's not really an issue with controls, but there's a point in SH4 where you stop visiting new locations and just revisit the old locations doing tedious tasks. It becomes quite repetitive, and I don't care about the characters enough in this one to feel motivated to finishing it again. It just feels like the second half of the game is padding. Saying that, I'm glad to have bought it again on GOG, and I do hope the rest of the franchise comes to GOG eventually (specifically 1, 2, and 3) but maybe that's just wishful thinking lol.
3. Oddworld: Munch's Oddysee.
I love this franchise so much, and I really do quite like this game, but they perfected the 3D controls with Stranger's Wrath. This one feels like they were trying to find their feet within a 3D world, and it's successful at times (I love the new additions, new creatures, new settings, etc) but it doesn't always work. Sometimes you have to fight the game camera to get a proper darn look at something; sometimes you run when you mean to walk, which can mean falling off a high ledge and having to walk all around again to where you once were; sometimes the actions are unresponsive or you get stuck doing a completely different action than what you intended (want to pick up a modokon? Don't be near anything or anyone else); etc. It's a flawed game that I don't think has aged as well as the other games in the franchise. Saying that, it's not necessarily aged badly either. I'd just like to warn that it tries to recreate the gameplay of the first two games within a 3d environment, and it feels as awkward as you might expect.