It starts with the App Store itself. The Close, Minimize, Zoom buttons (red, yellow, and green) are in a none standard location. It looks ugly. There is no title bar, and the toolbars are an ugly monochrome. This is just as bad as the new iTunes (vertical stoplight buttons, monochrome sidebar, nonstandard scroll bars).
Next up is the new Twitter for Mac app. Its not surprising its ugly, and its UI leaves much to be desired- its descended from Tweetie for Mac. That was one of the worst Twitter applications. It took a couple of versions to support Growl, and to send a tweet it was Shift-Enter which was incredible frustrating and stupid. See this post for more on that.
Back to Twitter- it has nonstandard stoplight buttons (sound familar?). It has no Titlebar OR toolbar- so how the heck does one move the window? By the ugly black box on the right. The font is in Helvetica, rather than the proper Lucida Grande. The new Tweet window is draggable by the bottom, and is not attached to the main window.
Because Apple has led the way with their bad UI design, other apps have also taken that approach. What a mess. For more on this, check out this post from Tim Morgan.