The classic RTS genre is in a major rut right now. There have been a few good games over the past several years, but I wouldn't say there are any standout hits.
My favorites have been the
8-Bit franchise (Armies, Hordes, Invaders) and
Tooth and Tail.
The 8-Bit games are from Petroglyph (former-Westwood guys) and play just like the old C&C games. What's really cool about them is that if you buy two of the games or even the entire franchise, you can mix and match the factions. Armies has two modern military factions, for example, and Hordes has fantasy humans and Orcs, so if you buy both Armies and Hordes then you can potentially have a modern military facing off against Warcraft-like Orcs. I highly recommend buying all three games just so that you can have access to all of the factions at once. It's a whole lot more fun that way, and the franchise pack only costs about 16 bucks.
Tooth and Tail is a unique RTS. Instead of controlling the camera, you control a single "general" unit and run around the map scouting and constructing buildings. When you want units to attack, you simply rally them to your location and send them forwards. Although this simplifies things quite a bit, there's still enough depth to allow for numerous strategies and give it lots of replay value. The game also plays beautifully with a controller, which is actually what it was built around (don't worry, M&KB still works fine).
Some other notable ones you can check out are: