Total Annihilation holds a big part in my history. It was a great game for one thing, but annihilated.com inspired me to get into running a website.
Thanks to TA and annihilated, I ran my own website based on a game (a Star Trek one), which at peak in 1999 was getting 2000 uniques a day. Taking USD cheques (like $40) from doubleclick into my UK bank in my school uniform in 1998ish was a unique experience.
Thanks to that experience it drove me to where I am today.
As far as actual RTS game play, Red Alert was best in my view. One disc for soviet, one for allied. Tanya, Dogs, and Tesla Coils. So many hours, so little to show for it.