If you use windows then
http://www.virtualdub.org/ will be a good tool to start with. It will do basic timelapses really easily and is the only program with a GUI that I can recommend.
If you want to do more complicated things then AviSynth is a really good tool.
http://en.wikipedia.org/wiki/AviSynth
http://sourceforge.net/projects/avisynth2/files/
It doesn't have a GUI, instead everything is done through script files - though the script files can be loaded through other programs as if the were a video themselves. e.g. you can load two videos in a script, blend them together, and then load the blended result into VirtualDub or Adobe premiere.
If you're on Linux or Mac then
ffmpeg is probably the best thing, though I haven't used it yet e.g.
http://programmer-art.org/articles/t...peg-time-lapse
On Mac, Linux and Windows you can also use ImageMagick:
http://www.imagemagick.org/script/index.php
This is probably the most powerful image editor, however it is probably far more powerful (and so confusing) than what you actually need.