There's just something about designing your own goodies that no strategy fan can resist. Games like Sword of the Stars or Galactic Civilizations 2 let you design your own spaceships for use in combat, but spaceship design is a common feature in space 4X games. It's not seen often in real-time strategy games, but unit design is definitely there, and the case-in-point for this loveable feature is Warzone 2100.
One of the earliest RTS games to support the custom units feature, Warzone 2100 is a blast from the past, and best of all, free and open-source. With a double whammy of free and retro, you can't really go wrong.