Sirtech's Jagged Alliance 2 remains an unsurpassed turn-based strategy experience, offering some of the most complex isometric battles the genre has ever seen.
Jagged Alliance 2 takes place in the fictional South American nation of Arulco. Taking the role of a mercenary, you've been hired by the country's deposed leader to retake the country from the hands of its tyrant, Deirdranna. With funds at your disposal and rewards for retaking towns and completing mission objectives, you can hire a mercenary crew and recruit the aid of local citizens and militia to reclaim Arulco. There's a rebellion, and you're leading it.
Like Final Fantasy Tactics, JA2 uses a strategic map screen where the player issues high level strategic orders. Unlike FFT, you're in control of more than a single group of units and you have to also supervise the the management of your liberated cities. Combat and individual location exploration takes place in tactical screen, where player can issue individual direct commands to their mercenaries. As the game is partly an RPG, you can train your mercenaries to be more efficient killers and equip them with gear that you salvage from enemies, receive as rewards or acquire through the online gun store. One of the more interesting elements of the game is its fake internet service, which is replete with websites to recruit new mercenaries and other services.
6. DISCIPLES 2
Disciples 2 is one of the few strategy games to feature a rich gothic motif. Set in a dark fantasy world (as opposed to a world of unicorns and rainbows), the main focus of D2's story revolves around four dominant races in a state of constant war. Included are the human Empire, the dwarven Mountain Clans, the demonic Legions of the Damned and the skeletal Undead Hordes. It's a setting much inspired by Warhammer Fantasy and as you may or may not know, nothing in that world is particularly pleasant.
Similar to Heroes of Might and Magic, the game is a mission-based strategy game with a focus on overland maps, and is spread across four separate campaigns whose stories tie into each other. The gist of the game is simple: you build up a Capital City that allows you to research new units and spells, using your heroes to lead armies to perform exploration and combat, and finally the battles themselves. Combat in the game plays out very similarly to Japanese turn-based RPGs like Ogre Battle where placement is everything. The combat is nothing at all like HOMM's.
5. HEROES OF MIGHT AND MAGIC 3
The third game in the Heroes of Might and Magic series takes off after the events of the second game where a bunch of stuff happened that nobody remembers or cares about. Story was never the series' strong point, and most of its appeal came from its great gameplay.
Like so many other empire-building strategy games at the time, the game was split into a number of different campaigns where you took possession over one of the game's many races. Every race came equipped with its own cities, which you built up for the purpose of recruiting new units while collecting an upkeep to maintain your forces. Every army was lead by a hero, whom you could train up by earning experience in and out of battle, giving them new skills and abilities each time they leveled up. Heroes also depended on the equipment you gave them--magical items scattered throughout the lands and carried by enemy heroes.
Battles played out on a field and your army was represented by unit stacks. Ten dragons could make a barbecue out of a thousand peasants while your other units sat back.
It was a game that deprived you of sleep every time you played it, not unlike every other game on this list.
4. SILENT STORM
It's the only tactical turn-based game that's set in WWII, a setting that's more or less overflowing with titles in every other genre. Heavily inspired by Jagged Alliance 2, at least in terms of combat (as there's no management mode), Silent Storm puts you in charge of a squad of allied commandos who infiltrate the German lines to destabilize their war effort.
The game is packed with tons of weapons from WW2 and throws in a bit of sci-fi towards the end with laser and gatling-gun wielding mechs. Crazy, I know.