No cropping.

$ ffmpeg -r 24 -pattern_type glob -i '*.JPG' -i IMG_%04d.JPG -s hd1080 -vcodec libx264 timelapse.mp4

Crop to 640x426 — works fairly well for social media.

ffmpeg -r 40.04 -i %03d.jpg -vf "crop=640:426:0:0" -vcodec libx264 -preset veryslow -tune stillimage -crf 23 -r 29.97 -pix_fmt yuv420p timelapse.mp4
-r 40.04 input framerate — choose based on number of images and desired length
-i %03d.jpg input file pattern
-vf "crop=640:426:0:0" crop (height:width:startx:starty)
-vcodec libx264 codec
-preset veryslow very slow (speed vs quality)
-tune stillimage for timelapses
-crf 23 23 is default, 0 is lossless
-r 29.97 final framerate — fixed
-pix_fmt yuv420p output format — required for some stupid players
timelapse.mp4 output name

More on the official wiki.