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The naan studio blog details the changes, and they are many. There's a dedicated tab for Twitter Lists now; you can follow and unfollow Lists, and check which Lists follow you. The new retweet functionality is now fully supported in addition to the old method, which lets you include commentary on what you're retweeting. You can also geotag your tweets now, and look at maps for your friends' geotagged tweets.
Echofon 3 also overhauls the app's search tab. You can search for users by first name, last name, username or company. Trends are easier to sort through, and searches you've saved at Twitter.com are accessible in the app. There are a bunch of other smaller changes, too.