GD2 has improved greatly with time (like adding gif support) but while I haven't tested them in about a year - ImageMagic/Graphics Magic uses much less memory for large images and outputs a much cleaner output. They also support a larger set of features and require less processing power.

It really depends on what you need them for - I'm not sure how to draw with imagemagic while I know how to do it with GD in php (though if you know neither I'd go with imagemagic). But whenever I need to generate thumbnails or work with photos I use imagemagic because I get a much better output quicker.