what operating system?

on linux i use the following for creating sd dvd images. it uses the 'mf' thing to pick up all the separate frames and stitch them together (a lot of the rest of the options are dvd specific. getting it into any format that youtube understands should be enough - it'll transcode it anyway.

Code:

mencoder "mf://@listfile.txt" \
  -oac lavc -ovc lavc -of mpeg -mpegopts format=dvd:tsaf \
  -vf scale=720:576,harddup -srate 48000 -af lavcresample=48000 \
  -lavcopts vcodec=mpeg2video:vrc_buf_size=1835:vrc_maxrate=9800:vbitrate=5000:keyint=15:vstrict=0:acodec=ac3:abitrate=192:aspect=4/3 -ofps 25 \
  -audiofile ${CLIP}_*.wav \
  -o ${CLIP}.mpg
 

where $CLIP is the basename of the project and listfile.txt contains the list of frames. and ${CLIP}_*.wav are the audio files to use

a quick google gives this post: http://forums.savage2.com/showthread.php?t=16672

which mentions these options for hd youtube:
Code:

mencoder
-vf scale=1280:768
-ofps 30000/1001
-ovc x264
-x264encopts subq=7:frameref=10:me=esa:partitions=all:8x8dct:bf rames=1:qcomp=1:bitrate=16800:pass=2
-of lavf
-lavfopts format=mp4
-o MySavageMovie.mp4 
 

that doesn't seem to be specifying an input file, so just plug the mf:// bit in there. i'd also generate my source images at the required resolution and drop the -vf scale.