From a sequence of images
mencoder mf://*.png -mf w=360:h=240:fps=12:type=png -of lavf -ffourcc FLV1 -ovc lavc -lavcopts vcodec=flv:acodec=mp3:abitrate=56 -srate 22050 -o outputfile
Obviously, replace the width, height, and frames per second above with the w/h/fps of your video. If you're using jpegs, use '*.jpeg' and 'type=jpeg' instead of png above. If you don't have any audio, use this:
mencoder mf://*.png -mf w=360:h=240:fps=12:type=png -of lavf -ffourcc FLV1 -ovc lavc -lavcopts vcodec=flv -o outputfile