Yes, we are now 40 years since first Atari ST machines went in sale (1985) .  Surely, development started earlier, at least 1 year. Main HW designer is same as designer of C64 (Shiraz Shiwji) - and 2 machines have pretty much differences. C64 was designed mostly for gaming, with HW support for it. Atari ST was designed for universal usage, good for hobby, gaming, programming, business SW, even some early CAD SW (mostly in high res.) . With then pretty advanced and acclaimed Motorola 68000 CPU, which price gradually went down. It was real 32-bit CPU, with 32-bit registers and operations, bit still with 16-bit data bus. On PC side there was Intel 80286 - 16 bit CPU, what meant max 64 KB addressable directly. They needed segmented programming - big drawback.  And Atari ST was with then huge 512 KB RAM.  I dare to say that it was first real home computer with hard disk port. What was with it before costed way more, so not for ordinary people.  It is called ACSI (Atari computer system interface) - and is actually early SCSI port system. With 8-bit data bus.
Was good for other things too, like laser printer. Top transfer speed of it is 2 MB/sec in peak (I measured it multiple times on different models, and it is it. Needed to write because lower speed is visible in different DOC, books) . Atari self made Megafile hard disk adapters - what actually converted ACSI to then actual SCSI (which has more pins, for instance) .
 But SCSI drives were pretty expensive in those years, so only small % of users bought it. And actually, average user did not need it really.
 Ports ? Yes, there was serial, parallel, of course joystick and mouse ports. And MIDI port - something not seen much even later. And of course floppy port.  Cheaper versions had only single sided floppy drive - max. some 400 KB capacity. And yes, in early years lot of SW was sold on single sided floppies, even if that meant on more disks.
 What is missing is universal expansion port (present on many 8-bitters then). I consider it as biggest flaw of Atari ST serial. It made diverse expansions, upgrades much harder to realise, meant usually need to open machine and do there even some solderings.

  Operating System (OS):  of course it was with support for usual FAT12 floppy data system, and even with FAT16 harddisk system (compatible until 32 MB partition size with then pretty much used (mostly on PCs) one. And of course there was GUI too (seen on Apple MAC then), called WIMP - Windows, icons, mouse, pull down menus.  All it was in 192 KB ROM - so not eating so much RAM (as usual solutions with loading OS in RAM)  -  but it delayed little, and very first Atari STs were with only small ROM, what booted OS from floppy. The reason was that they could not solve so fast to put all it in 192 KB ROM space.  Why 192 KB ? Well, surely because of ROM chip prices. It was cheaper to use 6x 32 KB than 2x 128 KB - what would solve fitting in. And when STE appeared in 1989 thay needed to expand it to 256 KB, but only in 2 chips (of course, prices changed). And there was another design flaw, what needed change of TOS ROM address space (start address) - should think ahead that it will need bigger capacity with newer HW and OS upgrades.
 Yeah, TOS versions :  so first so called floppy TOS 1.0 , then ROM TOS 1.00 (1985 summer), 1.02 - 1987 - Mega STE, added blitter support .  1.04 - 1989 - diverse updates, improvements. 1.06 1989 - STE TOS - very similar to 1.04.  1.62 - little later, fixed med. res. Desktop.inf bug  .  Then came TT - TOS 3.05 1991, 3.06 . Mega STE - TOS 2.05, 2.06 1992 . And Falcon - TOS 4.02 1993, 4.04 .   There was some work on Multi TOS, but it was not really finished, instead it Atari ST line manufacturing finished :-(
  Surely, one of main reasons was falling prices of PCs, manufactured by many firms, improved CPUs and other in them.

  In those some 8 years lot of SW, some expansions, upgrades appeared on market for Atari ST serial. Count of Atari SW is somewhere about 6000 programs by mine estimation. There is lot of freeware, shareware in it.  And some of it has harddisk install support in diverse ways. Of course, SW was distributed on floppies.

  And we are now in 2025, when SD cards have huge capacities, low prices. Surely, Flash cards are best way for some oldie - no need for extra power supply for hard disk, space for it ...
I was able to connect CF card to my Atari ST with IDE port somewhere in 2005 - and that was really nice experience (with much less capacity than later, of course).
  So, now big part of still Atari ST users has some SD card adapter with it. And + reason for it is that old floppy drives and disks are gone bad, unreliable.  
 I made floppy images of all my Atari ST floppies before 2000, knowing that they wont last much long.  And of course lot of other people. On Internet can DL almost all god old Atari ST SW as floppy image files. Will not go here in copy protection related things.
  And we are now at : what TOS version, what Flash card adapter, what hard disk driver SW, partitioning system to use now, for best working of old Atari SW ? Sure, some may come with: to run new(er) Atari ST SW . This later depends how newer SW is coded - with compatibility with old TOS versions, storage systems, or coded with some newer TOS replacement versions in mind ?  I will say it clearly: not interested in new Atari SW, maybe some games only. I will not use Atari ST, or even some accelerated one stronger model, as all it is very slooooow compared to today computer speeds (for masses), factor is surely over 1000 . Not to mention video and other things.
 And here we are at some 'expert opinions' :  use EmuTOS as it fixed diverse TOS bugs and runs Atari ST SW well (added some SW tests, but only small fragment of it) .
I tested lot of games with it, and what to say: disaster.  About some 30% worked not, worked with errors. Even Spectrum 512 failed (they did not care how TOS handles keyboard codes in some cases). And those work fine with regular TOS versions (except rarer some original TOS version compatibility problems). I wrote on my forum here about some really silly writings at Github. Old SW is buggy, TOS is buggy ...  That means insulting people who worked on it, and/or not knowing what term SW bug means ...  TOS was developed since 1984, mostly in C . And there were some standards used, and not those which came later (buggers did not have time machine) .  I have lot of experience with old Atari ST SW, with TOS versions. All it worked pretty well together on 99% cases.
   And some SW, even games had harddisk support, even program for hard disk installation.  And that was done with regular hard disk driver SW in mind, together with regular TOS versions - in which was filesystem code (FAT16 actually, as wrote compatible with widely used DOS FAT16 until 32 MB partition size). But it is possible to create TOS/DOS compatible partitions of bigger sizes with special parameters, and of course special driver SW for it. It is very useful for simple and fast data exchange, transfer with some modern computer (PC, Windows, Linux, MacOS - all they still support it) .
 Well, some made so called GemDrive system what allows Atari STs to access newer partition types, like FAT32, of bigger sizes.  It was first used in Steem emulator, called hard disk, and is actually assigning of some folder on host (modern computer) as Atari hard disk partition. But it works not in same way as regular Atari hard disk system. It is on filesystem level, actually it is extra code executed on host computer and not under emulated Atari - hooked to file function calls (Trap #1), it does LFN to 8.3 conversions too. All it is nice, but it is not full hard disk emulation, and many SW will not work with it. That's why Steem has real hard disk emulation too (via pasti.dll , using hard disk image files - up to 1 GB size, what is Basic ACSI max capacity) .  Same concept is used in Hatari (called GemDos hd emul.) And now there is 'GemDrive' in later ACSI2STM adapters, set as default. Surely based on Hatari sources. Well, use it if want, but be ready that not all old SW will work with it. For instance those using low level hard disk access.
 And to add, for slow Atari ST more smaller partitions are better than less big ones. Count of partitions does not affects speed (as some 'experts' wrote) .
  Now I'm in process to add few poductivity/util SW to hard disk adapted collection. Well, surely not much people will use them, and that's not goal actially, rather that people can see how they work, how that more than 20-30 years 'serious' SW looks ...
 
   

PP, July 22 2025.