Medieval II Total War would be the best in the series followed by RomeTW. Those two are a lot better than EmpireTW.
http://pc.ign.com/objects/800/800327.html (M2TW)
http://pc.ign.com/objects/498/498739.html (RTW)
You can also try Supreme Commander and its expansion.
http://pc.ign.com/objects/755/755287.html
You can also try Company of Heroes if you're into the whole war setting:
http://pc.ign.com/objects/743/743961.html
Can't really think of anymore off the top of my head. I rarely stick to an RTS for more than a month or two, but I remember those being pretty fun.
If you find something else, lemme know
