Once upon a time, I ran across VGMusic.com and noticed that they had lots of quality video game MIDIs available for download. I looked through and found songs from many games I had enjoyed in the past.
However, some of the songs I found were not as high quality as I thought they could be, so I figured I could do better and sequenced some MIDIs of my own.
All of my video game MIDIs are made by taking music rips/states/dumps (NSF/SPC/GYM or equivalent) and playing them back one channel at a time. I then input each track of the song into Noteworthy Composer, inserting instrument/volume/panning changes where appropriate. Once I'm done, I export it to a MIDI file.
Using this method, I've produced some extremely precise MIDIs, some of which could easily be mistaken (by inexperienced listeners) for automated conversions.