My favorite topic. Stop me if you have heard this before...
Chaos Strikes Back and its tutorial, Dungeon Master. While I don't think they are exactly underappreciated, they're still among the best games of the type.
Close Combat 2 is still unsurpassed in how the little men are ordered around. The commands you give are less absolute orders and more suggestions. You have to play it to understand what I mean.
Sid Meier's Gettysburg is still one of the most successful simplifications of grand strategy. Like Total War but absolutely zero fucking around on a campaign map.
Run 5 system from SSG is still one of my favorites for that scale of wargaming. It's one of the few where you actually feel like you're commanding an army instead of acting as its secretary. Culture shock may be too great for modern gamers. Try Panzer Battles or Rommel if any.
Balance of Power is one of the most interesting non-games I've ever played. Everyone should give it a go, just to see what gaming could be instead of what it is today. Warning: may cause depression and dissatisfaction in modern games.
Spellcross pit the armies of Earth against orcs, undead, elementals and wizards. The campaign is one of the best realized fantasy wargames in existence. While you start with infantry and tanks, as time goes on you'll incorporate psykers and mages into your forces. The opponent isn't stupid either, and as time goes on you may run into surprises as the forces of chaos have looted armories. Scenarios are varied, the game is suitably difficult, tech tree is surprisingly fun and most importantly, the campaign story is very immersive.
Magic: The Gathering (1997) is my favorite implementation of the card game into digital form. Despite all the bugs and oddities it's just great fun.
Master of Magic is the best Civilization game that isn't actually Civilization. Strange how hard it seems to modernize the basic idea.
Fantasy General is the best game in General series, oddly enough. Yet another game that could really do with a remake. Elven Legacy tries but falls just a little short.
The limitation to PC is a killer. Most of the really great forgotten games were on Amiga or C-64. Six-gun Shootout, 50 Mission Crush, Populous 2 (PC version was complete crap), Lords of Chaos, Airborne Ranger (again, PC version was crapola), Zoids, Theatre Europe (who remembers Midnight Sun?), Archon, M.U.L.E. and too many others to list.