The management of Preferences on the Linux desktop sucks, too. Or do I mean Administration? Although I know enough Linux users that I can find a defender of almost every bad UI choice, Ubuntu's Preferences/Administration is roundly acknowledged to be a clusterfuck. Especially by anyone who's used a Mac, which does to preferences pretty much exactly what search engines (rather than the early 1990s' "directories") did to the web, making it easy and quick to find what you want if you type what you know into a single text field. But even something as basic as Windows' Control Panel would be a step up.
On the Linux desktop, the user has to decide between "Preferences" and "Administration", and then between, say, "Keyboard" and "Keyboard Shortcuts", or "Network" and "Network Tools", or "Appearance", "Screen Resolution" and "Screensaver". They're being compressed slowly; "Appearance" contains what used to be multiple separate craplets, and instead of "just" two keyboard options, we used to have separate "Keyboard Accessibility" and "Keyboard Layout" choices. But there are still way too many choices to make, and each one is an expensive, painful choice that requires closing the newly-opened window and starting again from scratch if you choose wrong; not just hitting a back button. If you're going to make me guess, give me the fewest possible number of chances to guess wrong.
Better still, don't make me guess my way through your needlessly over-complicated UI at all; let me tell you what I know, and take me straight to the right place, or offer a short tightly-focused list of the likely possibilities if there's more than one.
Apple even goes as far as translating Windows terminology into Mac terminology, in an effort to be more helpful to strangers. Too many Linux users, if not developers, actively hate strangers, especially ones from the lands of Mac OS or Windows.
I count 40 choices on Ubuntu 8.04's "Preferences" and "Administration" menu. Even alphabetical order loses its usefulness when you don't know what word they'll have used. Or whether you're even on the correct 20-item menu.
Who thought that arbitrarily splitting "Preferences" and "Administration" was anything but a crutch to support the bad idea of an unworkable overload of piffling little applications? Stuff that doesn't make sense on a menu, and wants to be in a unified System Preferences or Control Panel application, depending on which background you came from. I'm sure someone, at some point, actually thought that lots of tiny programs was a better idea than one big one, but is it not time they admitted that it doesn't actually work out in practice, and we fixed this?
And don't get me started on the utterly useless crap that's the rest of the "System" menu!
Problem: too many cooks, no benevolent dictator.