Sorry I didn't have a link for MPEG4Modifier. I assume you found it online.
With regard to standalones:
QPEL and GMC are encoding options that most players won't play.
Custom Matrices can create sharper video, but some players do not like them either, and there are many different ones.
Packed Bitstream is a setting some claim makes smoother playback, but some players cannot tolerate.
B-frames are used to increase compression as they are smaller than I- and P-frames.
Square Pixels means the actual dimensions of the file, WxH detemine the aspect ratio. The aspect ratio in the avi header is rarely used to override the WXH for playback, but some players can only play those with square pixels, not just Custom 1:1, either.
The Modifier can be used to unpack and change to square pixels, and the info tells you if the other things are present.