If you like the HoMM games then you'll probably be interested in the Age of Wonders games.
I'll second this recommendation. Age of Wonders is an excellent choice for anyone who enjoyed the HOMM series. Disciples 2 is another similar game that I would definately recommend. Also, since you liked the Civ games you should definately check out Alpha Centauri if you haven't played it. The King's Bounty remakes are also quite good, although they're more tactical games than strategy games. You could also take a look at Spellforce, as it's a nice cross of RPG and RTS.
Moving into RPGs, pretty much all of the Infinity Engine games are recommended, as long as you don't have an aversion to AD&D (Baldur's Gate 1&2, Planescape: Torment, Icewind Dale 1&2). Temple of Elemental Evil is also recommended if you find you enjoy the D&D ruleset and want a game that emphasizes the more tactical elements of it. And I'd be remiss if I didn't recommend Arcanum while talking about isometric RPGs. Moving forward a few years, the Gothic series is highly recommended as alongside TES it's one of the most noteable open-world series out there. Gothic 1&2 show their age, but still remain excellent games; Gothic 3 is a bit newer and a good game once the community patch is applied, but doesn't quite rise to the level of the first two; and Risen, which is fairly recent, is a Gothic game in all but name and brings back a lot of kind of experience found in the first two games (just don't ask about Gothic 4... we don't speak of that). Vampire the Masquerade: Bloodlines is another excellent RPG that should definately be played if you get a chance. Same goes for Deus Ex. A few other fairly recent releases that should also be mentioned are Divinity 2: The Dragon Knight Saga (a sequel to Divine Divinity, and older game but also very good), and Drakensang: The River of Time. Neverwinter Nights 2 (particularly the Mask of the Betrayer expansion) is also quite good if you're looking for a more recent D&D based game (and the original NWN is also worth picking up, particularly for the many excellent user-made modules available for it).
And I'm sure others will continue to fill in many that I've left out. I'm afraid you're now facing a long list of excellent games that will take a ridiculous amount of time to get through.