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My favorite is Gentoo, even after all these years.
Sure, compiling stuff, tweaking all the config files, fixing the occasional broken compiles and so on is a major hassle at best and at worst it's enough to cause suicidal tendencies. But still, it's the most flexible distro of all as it can be tailored to almost any need whatsoever; you can harden the whole thing all the way from the bottom if you're paranoid, you can leave out printing, X, and so on if you just need console, you can include everything and the kitchen sink if you feel like it, and so on.
I use Gentoo on my server because I got tired with both Ubuntu and Fedora crapping all over themselves every now and then, and I especially hated how they insisted on replacing the changes I made to various config-files and scripts. Gentoo, on the other hand, doesn't try to override anything I've done and it works wonderfully as a server. On a similar note I've installed Gentoo on my N900 just to make a point to someone: Gentoo was very, very snappy on it and you could run SSH+Transmission (with 2 active torrents)+Web-interface for it+Samba server+Mumble with 4 users all simultaneously on it and you still had 40% CPU left -- quite a good example of how powerful the N900 still can be, and how well Gentoo can be made to fit such devices.
On the desktop I really have no favorite Linux-distro, however, as they all seem to come with all kinds of annoying shortcomings of their own, and then there's the simple fact that not all of my stuff has Linux-support anyways. Mostly I just use Ubuntu in a VM if I need something.