Here are a couple I like.

linuxquestions.org (a great site to read and get help on linux in general)
epicgaming.us (my main man Deven Gallo's site.)
dmusic.com (a good resource of free music, and if you make music yourself you can register an account and upload your stuff there.)
thebereancall.org (a Christian site with some interesting articles and a great weekly radio programme.)
toastytech.com (Though most of it is pretty old, it still gets a small update here and there. Apart from having a really interesting 'GUI gallery' with screenshots of old and new GUIs, much of the site is an interesting look at what websites looked like back around 1998 or so. And the guy who runs it is a really nice guy who responded to my emails when I emailed him.)

And that's all I can think of for now... but there's probably some more I haven't remembered.