Well this only took about three days to write...
ALLWMVFILES = $(wildcard */*.wmv)
RAWWMVFILES = $(wildcard */*raw*.wmv)
WMVFILES = $(filter-out $(RAWWMVFILES), $(ALLWMVFILES))
MP4FILES = $(addsuffix .mp4, $(basename $(WMVFILES)))
%.avi: %.wmv
mencoder $< -o $@ -ovc x264 -x264encopts bframes=1 -vf harddup -oac faac -faacopts br=160:mpeg=4 -channels 2 -srate 44100 -ofps 30
%.h264: %.avi
mplayer $< -dumpvideo -dumpfile $@
%.aac: %.avi
mplayer $< -dumpaudio -dumpfile $@
%.mp4: %.h264 %.aac
rm -f $@
mp4creator -create=$*.h264 -rate 30 $@
mp4creator -create=$*.aac $@
mp4creator -hint=1 $@
mp4creator -hint=2 $@
mp4creator -optimize $@
all: $(MP4FILES)
Then make all and watch the smoke come out the back of the machine.