Encode video for ipod classic

Question 1

You will probably have to re-encode because the iPod Classic can handle up to 640x480 according to the specs you provided, but your video is 1280x720. Video can be H.264, Baseline Profile, Level 3.0:

ffmpeg -i in.mp4 -vcodec libx264 -crf 23 -preset fast -profile:v baseline \
-level 3 -refs 6 -vf "scale=640:-1,pad=iw:480:0:(oh-ih)/2,format=yuv420p" \
-acodec copy output.mp4

Control quality with -crf and encoding speed with -preset. See the FFmpeg and x264 Encoding Guide for more info on those options.
-level currently does not set -refs for this encoder, so set it manually. There is a pending patch to resolve this so it should be fixed soon.
The scale video filter will scale the output to 640x360 in this case. The -1 value maintains the original 16:9 aspect ratio in the height dimension, while the 640 value sets the new width.
The pad video filter specifies the new maximum width and height of the video, plus the side-padding and top-padding in pixels. This is necessary to letterbox the original 16:9 video into the 4:3 aspect ratio required by the iPod classic. If this is not done then the iPod will expand the video to fit the screen height and will crop off the sides of the video during playback. To calculate the necessary values for for this parameter, consider that:
```
1280*x = 640 # x is the resize factor in the width dimension
x = 640/1280 = 0.5 # now we know x
720*x + 2*p = 480 # scaling the original video height by x, then adding
# equal padding p above and below the video must give the new desired
# video height of 480. solve for p
360 + 2*p = 480
p = 60
```
The format video filter will ensure that the output uses a compatible chroma subsampling scheme. ffmpeg attempts to avoid or minimize chroma subsampling by default when using libx264, but non-FFmpeg based players and devices do not support anything other than yuv420p, so including this will ensure compatibility. This is the same as using -pix_fmt yuv420p that you may see in other examples, but using format allows you to be specific as to where it will be applied in relation to other filters (not that it really matters too much in this case).
Since the audio is probably fine as is it can be stream copied (re-muxed) instead of re-encoded.

Question 2

since I was looking alot around to get ffmpeg conversion working for my iPod 5G, I just found info that was either outdated or did not work for me. So finally I stumbled upon some parameters that finally worked:

ffmpeg -i "INPUTFILE" \
    -f mp4 -vcodec mpeg4 \
    -vf scale=-2:320 \
    -maxrate 1536k -b:v 768 -qmin 3 -qmax 5 -bufsize 4096k -g 300 \
    -c:a aac -b:a 128k -ar 44100 -ac 2 \
    "OUTPUTFILE.mp4"

Some remarks:

for scale, I let ffmpeg scale it to a height of 320 although the display is just 320x240 or the iPod supports up to 480. 320 is for me the Sweet spot, because the files are a bit smaller and they also sync to an iPod Touch which has a Screen of 480x320.
The Audio quality can be changed if needed.
I did not try touching the other parameters as they work fine and produce decent results.

EDIT I modified the command a tiny bit, as I had problems with some files which had audio tracks encoded in 48khz and more than 2 channels.

Question 3

ffmpeg.exe -i "Video.mp4" -vcodec libx264 -preset fast -profile:v baseline -lossless 1 -vf "scale=720:540,setsar=1,pad=720:540:0:0" -acodec aac -ac 2 -ar 22050 -ab 48k "Video (SD).mp4"