Not on GOG, but I highly recommend WH40K: Dawn of War and its expansion Dark Crusade. It's pretty close to a standard RTS formula.
DoW2, which is more of a RTT than RTS had active pause but it got somewhat broken in one of the patches and second expansion removed it entirely.
Total War games also generally have this feature, but I'm not sure if it is available in all instalments or not.
Personally I really like when games have this, since micromanagement is not my strong point. That's why I hate what was done in Starcraft 2, where higher difficulties locked the game speed to maximum. I finished Warcraft 3 FT on hard, but I don't think that I'll be giving brutal difficulty a chance in SC2.