The Atari ST series had a mainly build-in, ROM-based (only early versions originally booted off floppy disks) Operating System - slightly based on CP/M-68K - named GEMDOS, and a GUI from Digital Research, GEM. Combined, it was named TOS (Tramiel Operating System).
TOS existed for the ST series in many versions, from 1.04 up to 2.06.
The later versions 3.x and 4.x were made for the TT/Falcon series.
GEM was something what some people called "Poor mans Macintosh OS", but for sure it was created a long time before a usable Version of Microsoft Windows appeared.
A list of TOS revisions (in detail !) can be found >here< ...
(archive.org mirror >here<).
Some really important utilities
Lacom SD-System 3.2 (e.g. for Lacom's Syquest SQ-555 drives)
(this driver is working with AHDI but also with newer HDDRIVER)
AHDI 6.061 (Atari Corp.) HD driver software (.ST disk image)
CHBD 5.02 self extracting archive Claus Brod's HD driver from the book "Scheibenkleister" ... see also his own pages
Uwe Seimet's HDDRIVER (not for free, demo only, but sophisticated HD driver with PC formatted partition support a.o. features)
Important to write (and read) .ST disk images:
Floppy Imaging & file transfer from P. Putnik
(it uses Simon Owen's fdrawcmd, runs at least with Windows XP)
MSA Converter (for .ST disk images)
ST ZIP as an essential packer/unpacker
UNRAR famous PC unpacker program
(not compatible with newer RAR archives >= v3.0)
Kermit File Transfer program from Columbia University
Oberon V4 for the Atari ST
Oberon-2 Compiler V1.22 for the ST
Alice PASCAL for the Atari ST
ENCOM all stuff you can think related to GFA BASIC
A free C compiler to replace Pure C from Henk Robbers
Pure C (and other compiler, page says Pure C 1.1 but it's 1.0)
A Forth Interpreter/compiler for ST(E)'s, and some demos
Megamax Modula 2 still available also
Atari ST M2 68 Modula-2 Development System 1.0 ...
... splitted in Disk 1 2 3 4 and an emacs disk
Sozobon C Compiler 2.0 (single files) or as an LZH archive here ...
Sozobon is similar to a "pimped" Small C and comes with sources (!)
GCC for GEM/TOS/MagiC (french web page)
BC-FORTRAN77 Version C
Perl 4.0 Patchlevel 19 in two versions
ELAN-1 Programming Environment 1.5 for the ST
APL 68000 and some APL source files
Cross Assemblers for 6800-6811,8085,Z80
The Frankenstein Cross Assemblers V2.1 for about 20 CPUs
Special applications / OS replacements
photochrome - a sophisticated graphics converter (for STE's), can show up to 4096 colors simultaneously.
Teradesk - the only open-source desktop for the ST
MiNT Software (with a newer version of GCC !!)
FreeMiNT Portal (EasyMiNT, CrippleMiNT, gemlib a.s.o.)
massi Soft (german, useful HowTo's to EasyMiNT, CrippleMiNT)
The unofficial XaAES (MiNT successor) page
MultiTOS system disks (for Falcon030)
MagiC (from Application Systems Heidelberg - commercial)
MultiGEM II (Maxon MultiGEM II - meanwhile N.AES - as .MSA file)
Remember: MiNT on a plain ST is almost impossible or at least not very useful... I recommend MagiC or Teradesk only for a ST(E).
An old MINIX port for the Atari ST is also available
And a disk for STs of Minix demo programs also
nroff Docu for installation: here
Some other docu info here
A helpful blog entry here
MacMinix with PDF documents of the manual here
Another source of Minix disks here
Some GNU stuff for MINIX here
C68 C-Compiler for MINIX here
MINIX 68k stuff here
Links to other software pages
Applications & more:
ftp.cs.tu-berlin.de/pub/atari/ (misc. ST software)
www.umich.edu/~archive/atari/ (misc. ST software)
chapelie.rma.ac.be/atari/ (misc. ST software, not the same as above)
ftp.lip6.fr/pub/atari/ (again another misc. ST software site)
kurobox.serveftp.net (and this seems to be another mirror)
A fine selection of software links named U.T.S.I. comes from "Bolles", unfortunately a handful links doesn't work anymore
Useful freeware utilities from Draconis
Karsten Luedersens pages with interesting tools
Cyberstrider's software page (unfortunately now only from archive.org)
haretuerk's Atari apps page
Atari Museum downloads
Michael Bernsteins useful tools
freddo.chez.com very interesting collection of tools
Games & more:
A Scumm VM for the Atari ST (easy d/l link for the related ZIP), and the related Scumm VM homepage ...
A nice game similar to MidiMaze named "Cyber Race" (2 players possible, but unfortunately only for 68020 CPUs and above, don't know why)
A site named atari.8bitchip.info with harddisk adapted (patched) games
A second site with hard drive adapted ST games: Klaz's Hideaway
Atarimania Games and a few utilities at a glance
AtariLegend - Games overview (and d/l if you register)
Theoldcomputer ("ROM" site for Atari ST programs)
PlanetEMU (a great repository, also for games)
Get-your-ROM ("ROM" site for Atari ST programs)
EmuParadise ("ROM" site for Atari ST programs)
gametronik.com ("ROM" site, also for Atari ST)
<more links will follow soon>
<This page is still under construction>