Check out the Wargame series. It's all Cold War "what if" stuff, and If I recall, the most recent release, Red Dragon, takes place in a 90's like setting.
It's more RTT than RTS though, so less resource micromanagement and base building, more emphasis on individual units, tactical movement, and complex combined arms strategy.
I can't really think of any classic RTS type games with a modem setting. Closest I can get is WWII.