Hi,
I also was about to suggest vexflow, but someone beat me to it :-).
I've recently started studying species counterpoint and actually was looking for something which you provide on your website :-) . The applets don't show here though (linux, chrome). I'd appreciate it if you'd let me know when/if HTML5 and _javascript_ conversion gets done :-D .
On a sidenote (perhaps for a different topic), in Musescore there is the possibility to create plugins which provide harmony checks, someone also did a plugin for a previous Musescore version which checked only first species counterpoint.
I know lilypond's first purpose is creating sheet music, not composing music, but are there snippets of scheme or libraries around which could do the same?
I think, for people who study counterpoint and voice leading, or any other rule-set in music, it would be very interesting to have a an option to check if they've followed the rules. In my case I have no teacher, can't afford private lessons, so I have to figure it out on my own without any way to check if I'm actually correct in interpreting the rules and executing the exercises.
grtz,
Bart