I haven't decided about the best way to do Fux's counterpoint exercises. I copied the first few down on music paper. (There's lots of good blank staff paper available online. For two-voice counterpoint, I've been using the "instrumental duet" sheet from this extensive collection of blanks. As things get more complicated, there will be increasing returns from a software score editor, though.
I spent a while today running down some score editors for GNU/Linux. I want something with a reasonably intuitive graphical interface that can also output lilypond format. (I wonder if it might be fun to make a blank workbook of Fux's exercises as I do them. If so, I'll want lilypond markup for that, and I hate the idea of duplicating work.) It looks like the best option is probably NtEd, so I think I'll start with that.
I also stumbled on a web program called noteflight that looks like it will be great for sharing work on this blog. I don't think I can use it as my primary editor, but I'll probably do up some occasional samples. Like this, my favorite of the four exercises I've done so far:
That's in the dorian mode, with the counterpoint below the cantus firmus. It sounds nice!