The crackling issue in Zynaddsubfx that I described earlier is supposed to be solved in Yoshimi, a Zynaddsubfx fork/derivative. There is even a package for it in the Ubuntu repositories, so I gave it a try.
However, I could not connect my MIDI controller (the AKAI MPK mini) to it. Why? Because the controller shows up in Qjackctl's ALSA tab, while Yoshimi is in the MIDI tab. Patchage and a2jmidid don't help, either. Apparantly the exact same problem goes for Bristol, simulator of classic organs and synths.
My MIDI controller is connected through USB, my audio interface is connected through Firewire. Thus I use the firewire driver in jack. I wonder if there is any way of making the controller work with Jack MIDI clients. I mean, OK, Jack MIDI is the new thing and ALSA midi may become obsolete. In any case it would be nice to still be able to use my USB MIDI controller, and I figure there has to be a solution.
EDIT: Starting Bristol with the "-midi alsa" option, or Yoshimi with the "-a" option does the trick. The apps will then show up in Qjackctl's ALSA tab.