Earlier quoted context omitted.
I'd prefer 3.0 - because it was the baseline to DOS applications, it seems. EverythingTM runs on DOS 3.0. (I'm using MS-DOS 5.0 on my 386, though.)
I'm with you there -- IIRC, the 3.x series was all about hard disks. I'd lean toward 3.31, though, personally as the "Everything(TM)" item since (I think) that was the version that shipped with FAT16 (had to hit up Wikipedia and this was the version that supported partitions over 32MB). I remember, as a kid, that we had to have 2 partitions on our drive because of the version of DOS not supporting partitions greater…
I suspect the most useful thing I wrote was a simple "undeleter" program, for recovering deleted files from floppies and drives. Unmarking the FAT-entry as deleted, then chasing blocks to reassemble the file.