use a loop
If you're a Linux or OS X user then you can use a Bash for loop:
mkdir outputdir
for f in *.mp4; do ffmpeg -i "$f" -c:v libx264 -vf scale=640:-2 -c:a copy "outputdir/${f%.*}.mp4"; done
Maybe a Windows user can add a similar example that works for that OS.
or simply cram it all in one command
ffmpeg -i 1.mp4 -i 2.mp4 -i 3.mp4 -i 4.mp4 \
-map 0 -s 640x480 -c:a copy 1_2.mp4 \
-map 1 -s 640x480 -c:a copy 2_2.mp4 \
-map 2 -s 640x480 -c:a copy 3_2.mp4 \
-map 3 -s 640x480 -c:a copy 4_2.mp4
You have to use -map
otherwise the default stream selection will choose the same input for each output.