While it was a nice program, I don't think it's been updated since 2007, and even then I think there were better (and free) apps out there for conversion. SUPER might be a pain in the balls to download, but when I used it it was a very nice converter.
Since my XBox is dead and I no longer watch video through XBMC, I haven't had need to convert or hard-sub videos since ZoomPlayer + CCCP plays 99.9% of my files flawlessly (I have SOME blocking issues with SGKK's encodes of Bleach when manually skipping, but I think that might be due to CoreAVC/CUDA)
Given that you're asking this under the NDS section, I'm going to have to assume your goal is to play video on the DS, I would highly suggest forgetting about converting to AVI (or at least as an end result) and suggest you use Moonshell2 and DPG.
Moonshell2 comes with a DPG converter, but I don't think it does a whole lot in terms of extras (it does not support soft subtitles).
BatchDPG is a better utility, it lets you select audio and subtitle tracks and has more encoding options.
If you're going to be working with MKV files (nice for PC, not so nice for small mobile devices) you should learn how to extract the video/audio/subs manually and use them to convert to the format of your choice.
Get MKVtoolnix (extract to your location) MKVExtractGUI (extract the files in the MKVExtractGUI folder to the MKVtoolnix folder) then run MKVExtractGUI.exe, when you open your file it will show you everything inside including custom fonts and chapters. You can choose to extract whatever you want and use them in your conversion app.