Dune II.
NO questions asked. Its plot and gameplay outclass any RTS to date. Like most old great games, it was designed with gameplay in mind, not just purty graphics.
Kept me addicted for years. Never did finish it will all 3 houses though. When I was really young and first played it, i found mission 5 and 7 hard for most houses. Missle Launchers and Ornithopters were my worst enemy. When I replayed it when I was a little older, probably around 1997, it was challenging and amazingly good fun.
The computer, although they always started with massive forces, never seemed to cheat apart from their random reinforcement drops next to your base early on. Dune2000 and Emperor were poor remakes. They diverted too far from the classic.... probably trying to address some possible balancing issues for multiplayer.
They turned the Siege Tank into Red Alerts artillery for gods sake!!! The equivilent of a Mammoth reduced to a pitiful artillery piece.
To be strictly honest, you CANNOT have a 'THE BEST' game. You can have the best game for a genre but comparing Dune II to Half Life or to Civilisation 1/2 is like comparing apples to pears.