- A music composer that took advantage of the MIDI ports. Connecting the software to synths etc would allow the Atari ST to not only control the synth, but also to record the music in note form as it was played.
- A BASIC interpreting environment. Noteworthy for no reason other than this was the place where I wrote my first program ever.
- A desktop publishing application with similar functions to the early Pagemaker.
Cubase or C-Lab Notator.
> A BASIC interpreting environment.
> A desktop publishing application
This may be Calamus. Interesting fact: "an Atari Desktop Publishing system consisting of an Atari Mega ST computer, mono hi-res monitor, SLM804 printer and desktop publishing software cost less then an IBM or Apple laser printer alone." 
Atari ST MIDI stuff, with screenshots: http://www.atari-music.fddvoron.name/timidi.htm - Cubase was the famous one, but since the ST had MIDI ports built in there was no shortage of others.
GFA Basic was a popular Atari ST replacement
Calamus? Although it never struck me as horrible as PageMutilator.
GFA basic or Hisoft basic (along with the many other dev languages that Hisoft had)
Calligrapher in the UK, Pagestream, Calamus.
And probably PageSteam for the the desktop publishing app.
Not sure on that MIDI composer.
but both were really awesome compared to what existed on other platforms back then. In particular, I liked their documentation. Those were great times for documentation (not just BASIC, also TOS, GEM etc from that time more than today's. Either there were more qualified tech writers per product, or the products were simpler ... or maybe just nostalgia.
Learned Atari basic from a 2 page leaflet that came with my 800XL when I was 8, then progressed through True Basic and GFA Basic.
Apps I remember:
Revenge of the Mutant Camels remains one of the best games ever.
Calamus was also a great piece of software that predated Pagemaker for many years.
Heroes quest, police quest series of games.
There was an animation/tweenijg app for animation that blew me away.
These machines were great substitutes for amigas of the day.
Calamus -- at least as a brand -- outlived PageMaker, though! Invers Software, the owners of Calamus, shut their doors only last year, but the web site is still up; a macOS descendant of Calamus called "iCalamus" appears to still be in active development, under relatively new owners (who are longtime Macintosh developers).
They did some really nice things with virtual objects, being able to zoom in down to a printer dot, stochastic rasterization and all that.
There were some other very high-end packages for Atari as well --Didot, Retouche Pro, TMS Cranach. For some reason European developers really went wild developing professional-level DTP software for Atari with some very impressive results. Too bad Tramiels didn't do much to support them...
I might have to look up the Mac version
I'd load the whole of U6 from 4 floppy disks, then fire it up and play, and when done, I'd save my position and copy it all back to the 4 floppy disks!
What helped were 2 things:
*Utility to format disks to high capacity
*Fast shareware disk copy utility
I'd really love to boot up Spectrum Holobyte's Falcon again, but with the CPU clock goosed up so it could get higher framerates...
Unlike EmuTOS, AmigaOS is still closed, proprietary code.
Unlike Hatari, we've got winuae (windows-only) and a bunch of feature-cut, special purpose and/or abandoned ports to other platforms.
I never had an Atari ST (stayed with Commodore to the bitter end, plus Tandy happened soon after) but I am glad someone out there is dedicated to keeping these 16/32-bit computers alive.