I'm very picky about my desktop environment. I like windows, toolbars, icons, etc. to be arranged in a certain way. Typically, I turn off annoying prompts and nag screens in Windows, and unhide "scary" advanced options in OS X. One hard-to-fix pet peeve is when applications put an icon in the notification area (near the clock) AND leave a tab in the taskbar. This wastes valuable taskbar real estate.
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