I have a few. And most of these are because of mods.
Rome: Total War. Hands down still the best of the Total War series. It was the first 3D total war Game too so it was pretty special. While the vanilla game hasn't aged quite as well in the graphics department, mods like Roma Surrectum look better than some of the more recent total war games and have fantastic gameplay. The AI is still as dumb as it's ever been, but it has the best battle engine of the series.
Dawn of War: A truly great RTS and the best 40K game they have made so far. All the races play similar but also each take time to master and each army caters to a different playstyle. The animations for the units are all still absolutely fantastic. Combine it with some race and update mods (The SM's haven't aged as well as the others) and it is even better.
Doom 1/2: This one is also mainly because of mods. Doom still plays pretty great, but it's the user made levels and mods that really make it fantastic. Mapsets like Back to Saturn X and mods like Weapon X, Guncaster and Project MSX make Doom play however you want it to play. Be it like a modern shooter with aiming, give you a Crysis style suit, or a shooter RPG where you play as a gun wielding dragon. Probably my favourite shooter of all time.
Half Life: Still the best story shooter out there. While the graphics have aged a bit, nothing mods can't fix if you want to. I always preferred the original to 2 as well, just something about it that I can't quite put my finger on makes it much better.
Resident Evil 4: Still the best action horror game there is. It's amazing how well it still holds up today. Especially when compared to 5 and 6, which weren't great to say the least.
Battlefield 2: Yes, another one because of mods. But Project Reality make it the best modern shooter, and Forgotten Hope the best WW2 shooter. Although online does work for these 2 mods, I only play the singleplayer, and the bots are surprisingly good. This one really is because of just those mods, ans Battlefield 2 itself hasn't aged all that well.
Call of Duty 1 & 2: Yes, CoD, it sucks bla bla bla. But the first 2 had some of the best WW2 Solo campaigns out there.
Starship Troopers: Terran Ascendancy: A Starship Troopers RTS that hardly anyone knows about. Despite being not all that well received, I personally love it. Commanding a small squad and killing loads of bugs, with an RPG system for your troops. That and the cool mech suits make it as fun as ever for me. It's now shareware I believe, so you can download and play it for free.
Future Cop: LAPD: Another one many haven't heard of, but very fun. Having a mech that can transform into a car is pretty cool, and the gameplay still holds up, both campaign and the strategy mode.
Starfox 64: My favourite childhood game. It was great getting this in my hands again when I got a 3DS. It's criminal they haven't made more yet. The gameplay is truly timeless.
Super Mario All Stars: Because Mario is fun and always will be. Period.