An article on IGN has some info about possible plans for some form of Total Annihilation follow-up gleaned from a talk by Gas Powered Games' Chris Taylor, designer on the RTS while at Cavedog. Here's a bit on what was said, though they admit it's not clear whether this refers to a true Total Annihilation sequel, or just an RTS game in the same vein:

While Taylor said he couldn't give too many details to the crowd, he did confirm that Gas Powered Games was working on "an RTS follow-up to Total Annihilation."

Taylor also confirmed that the game already had a publisher, but wouldn't say who it was. He did, however, mention that it was "a big one... one that doesn't also publish operating systems." This is obviously a reference to Microsoft, publisher of Gas Powered Games' Dungeon Siege.