The following tools and methods are how I am currently using Twitter:-

• TwitterFeed & Ping.fm -- TwitterFeed will tweet your RSS feeds, however it can also send the feeds to Ping.fm which is how i use it. Ping.fm will post to other sites as well as Twitter. Both TwitterFeed and Ping.fm will cloak the URL to save space. By using this method anything I post to the sites I'm promoting will also be added to Twitter and a few other sites.
• TweetLater -- Can be used to auto follow people that have followed you and also tweets can be scheduled. I've only used it for the auto follow feature so far and it is a real time saver.
• Yoono -- Is just one of countless applications to keep track of tweets, I use it because it is a collapasble Firefox plugin that also keeps track of RSS feeds like Google Alerts for me. It can also connect to other social networks like Facebook.
• TwittyTunes -- Is another Firefox plugin that hooks into the FoxyTunes Firefox plugin. I use it to post tweets showing what music I'm listening to and web pages I'm browsing.
• Tweeter Getter -- This is a viral way of building your followers. It hasn't been very successful for me yet but I haven't promoted the link too much either.
• Twitter Grader -- Will give you a rating of your Twitter account. I think some of my followers have come from following grader although I could be wrong...
• Twitter Counter -- Twitter Counter shows stats about your Twitter account and also has widgets for promoting your Twitter page.
• Twitoria -- Find who amongst your followers is active.

There are a lot more applications for Twitter that I'm yet to look into if I find something useful that helps automate Twitter I'll add it to the list above list...