I use ImageMagick for that sort of thing - a real swiss army knife of image processing. It has a command line interface which makes doing repetitive tasks and handling arbitrarily large numbers of files easy. For what you want you would do something like:
convert -delay 10 *.fit animation.gif
I use it under Unix/Linux, but there are DOS and Windows versions out as well. It's free GPL software.
http://www.imagemagick.org