I have been using Twitter for a while now and run across all kinds of sites out there for Twitter using the API or giving stuff to help improve your Twitter profile. Here is a list of the one that I remeber running across. If you have more sites that you think I should add email me.
me[at]kellykarnetsky[dot]com

Improve Your Profile Visually

TwitterPatterns – Free background patterns for Twitter
MyTweetSpace – Twitter profile themes
TwitterBacks – Free Twitter backgrounds
TwitBacks – Make your own Twitter background
Bubble Tweet – Create a little bubble shaped video on your Twitter profile page

Following & Un-Followers

Twellow – Directory of users to connect with
Tweeple Twak – Keep an eye on followers, trends and un-followers
Just Tweet It – Twitter user directory
Mr. Tweet – Helps you build relationships on Twitter (not a dating site)
Twollow – Auto follow people who follow you
Qwitter – Find out why people stop following you

URL Shortening

TwitPwr – Short URL service just for Twitter

Marketplace

Tweba – Twitter marketplace, like eBay

Charts, Clouds & Trends

TwitterCounter – Charts out how many followers you get per day and stuff
TwitterSheep – Tag cloud made from followers’ bio’s
Twitemperature – Lets you know if you talk about the hot topics on Twitter
Re.Twit’d – Shows re-tweets and how many times they were re-tweeted
Twitturly – Track what URLs people are talking about as they talk about them
Twitscoop – What’s hot on Twitter right now
StockTwits – Talk about stocks, stuff like that
TwitterFriends – See who you reply to the most and the most that reply to you
Twitbits – Get information on users

Your Worth & Fun Stuff

TweetValue – Find out how much you are worth, not as much as Obama though
Twitter Grader – Grade Twitter users
Twit or Fit – I guess like Hot or Not, the site asks you what you want it to be?
Twitterank – Like Google’s Page Rank for Twitter

Real Time Feeds

TwitterVision – Showing tweets around the world in real time
CurseBird – Real time feed of cursing on Twitter

Make Money Using Twitter

Magpie – Earn money from advertisers
Twittad – Sell your background and get paid

Tracking & Replies

Twittertise – Advertise and track your success
Twply – Get Twitter replies in your inbox
Twilert – Like Google alert’s but for Twitter
Tweetburner – Track links you share on Twitter

Tweeting

TweetWrappr – It wraps your tweets in a present
Twitwall – A easy blog for Twitter users
Splitweet – Post to multiple Twitter accounts
Snipt – Share snippets of code on Twitter
Tweet Later – Schedule tweets, basically automated tweeting

Miscellaneous

TweetScan – Download all of your tweets