Yes you can. There are multiple websites (such as kraken, btc-e and cryptsy) which support API, where you can trade altcoins for BTC or USD/EUR. I am not sure what you mean with a bitcoin daemon, but I think you mean a script or something like that. You can use multiple programming languages to use the API, as shown on this example page on kraken.

After you got something working, you can trade anything you want, as long as there is a market on the specific exchange site you are using. Good luck!

edit: Ahh I see now what bitcoind is. Of course you can implement this in your script to use for your market strategy, but I don't think you can buy or sell directly from there, as it is not connected to an exchange site.