There are several programs that allow an MS-DOS system to work with an
Atari-format 5.25" diskette.  Most of these work with the Atari SS/DD 180KiB
format.

There is also a device, detailed below, that allows an external 5.25" floppy
disk drive to be connected to a modern PC via a USB port, and which supports
reading Atari DOS 2 SS/DD 90KiB floppy disks. 

Atari-Link PC (AtariDsk) V1.2 (c) 95-12-09
==========================================
  by HiassofT (Matthias Reichl)
  Ataridsk is a program for MSDOS-PCs that allows you to access Atari floppy
  disks in double density (180KiB).  All you need is a PC (XT or 286 should be
  sufficient) and a 5.25" floppy drive.  Features of this tool:
    * Menu driven user interface
    * Read, write and format Atari disks on the PC
    * Small size (only 35KiB)
  http://www.horus.com/~hias/atari/

WriteAtr V0.92b
===============
  by HiassofT (Matthias Reichl)
  With WriteAtr you can write double density ATR-images to Atari floppy disks
  on your MSDOS-PC.  You can also create ATR-images of double density floppy
  disks!  All you need is a PC and a 5.25" and/or a 3.5" floppy drive.
  Version 0.92b added experimental support for the enhanced density (1040
  sectors/128 bytes per sector) format.  Please note: this format doesn't work
  with a lot of floppy controllers - use it at your own risk!
  http://www.horus.com/~hias/atari/

MyUTIL
======
 - By Mark K Vallevand
 - Based on Charles Marslett's UTIL.
 - http://www.umich.edu/~archive/atari/8bit/Diskutils/Transfer/myutil.zip
 - Includes SpartaDOS disk utility v0.1e to access 180KiB SpartaDOS disks

ATARIO
======
 - By Dave Brandman with Kevin White
 - Reads SS/DD 180KiB Atari disks.
 - www.umich.edu/~archive/atari/8bit/Unverified/Diskutils-redist/atario21.arc

SpartaRead
==========
 - By Oscar Fowler
 - Reads SS/DD 180KiB SpartaDOS disks.
 - http://www.umich.edu/~archive/atari/8bit/Diskutils/Transfer/sr.arc

UTIL
====
 - By Charles Marslett
 - Reads/Writes SS/DD 180KiB Atari disks.
  http://www.wordmark.org/

===============================================================
Here's some advice on using the above utilities from Hans Breitenlohner:

There are two technical obstacles to interchanging disks between
DD Atari drives and PC drives.

1. The Atari drive spins slightly slower (288 RPM instead of 300 RPM).
   If you format a disk on the Atari, then write sectors on the PC, it is
   possible that the header of the next physical sector will be overwritten,
   making that sector unreadable.  (The next physical sector is usually
   the current logical sector+2).  The solution to this is to format all
   disks on the PC.
       (Aside:  Does anybody know how this problem is handled on the
        XF551?  Is it also slowed down?)
     Konrad Kokoszkiewicz answers:
     "The XF551 disk drive is not slowed down - these drives are spinning
     300 rotations per minute.  To prevent troubles with read/write disks
     formatted and written on normal Atari drives (288 rot/min), the main
     crystal frequency for the floppy disk controller is 8.333MHz
     (not 8MHz, as in 1050, for example)."

2. If the PC drive is a 1200KiB drive there is the additional problem of the
   track width.
   The following is generally true in the PC world:
    - disks written on 360KiB drives can be read on either drive
    - blank disk formatted and written on 1200KiB drives can be read on
      either kind
    - disks written on a 360KiB drive, and overwritten on a 1200KiB drive,
      can be read reliably only on a 1200KiB drive.
    - disks previously formatted on a 360KiB drive, or formatted as 1200KiB,
      and then reformatted on a 1200KiB drive to 360KiB, can be read reliably
      only on a 1200KiB drive.
   (All this assumes you are using DD media, not HD.)

   Solution: Use a 360KiB drive if you can.  If not, format disks on the
   Atari for Atari to PC transfers, format truly blank disks on the PC
   for PC to Atari transfers.

Jon D. Melbo sums it up this way:
   So a basic rule of thumb when sharing 360KiB floppies among 360KiB &
   1200KiB drives is: Never do any writes with a 1200KiB drive to a disk that
   has been previously written to in a 360KiB drive....UNLESS... you only
   plan on ever using that disk in the 1200KiB drive from then on out.  Of
   course a disk can be reformatted in a particular drive any time for use
   in that drive.  As long as you follow that rule, you can utilize the
   backward compatible 360KiB modes that most 1200KiB drives offer.

AnaDisk + DeAna
===============
While the above mentioned utilities work with SS/DD 180KiB Atari-format disks
or SS/DD 180KiB SpartaDOS disks, the following combination of utilities has
been used successfully to read SS/SD 90KiB Atari-format disks.  So if you only
have standard Atari 810 and/or Atari 1050 drives, you could look into:

AnaDisk -- now a product of New Technoligies Inc. (NTI)
See: http://www.forensics-intl.com/anadisk.html
The current version is "not made available to the general public" (!)
Previously a product of Chuck Guzis @ Sydex, http://www.sydex.com/
Older versions available: http://ch.twi.tudelft.nl/~sidney/atari/
- Reads/Writes "any" 5.25" diskette

DeAna by Nate Monson
Available: http://ch.twi.tudelft.nl/~sidney/atari/
- converts AnaDisk dump files from Atari format

See http://ch.twi.tudelft.nl/~sidney/atari/ for tips on using this
combination of utilities.

Preston Crow writes:
  "As best as I can figure it out, if your PC drive happens to read
  FM disks (I'm not sure what the criteria for that is), then you
  can read single density disks on your PC by dumping the contents
  to a file with AnaDisk, and then using Deana.com to convert the
  dump file into a usable format.

  For enhanced density disks, Anadisk generally only reads the first
  portion of each sector, but it demonstrates that it is possible for
  a PC drive to read enhanced density disks."

FC5025 USB 5.25" floppy controller
==================================
 - By Device Side Data
 - Plugs into any computer's USB port and enables you to read data
   from an external 5.25" floppy drive. 
 - Sold as a controller board only without a drive mechanism.
   It has been tested to work well with the TEAC FD-55GFR drive and should
   also work with most other 5.25" drives.
 - The FC5025 is read-only.  It cannot write to floppies.
 - The FC5025 may be unable to read disks that are damaged or copy-protected.
 - The FC5025 is intended for 5.25" disks only, not 3.5" or 8" disks.
 - The FC5025 may be unable to read the second side of "flippy" disks,
   depending on the drive it is attached to.
 - The included software works on: Linux, Mac OS X, Windows
 - The included software supports types of disk including: Atari 810
 - Available: http://www.deviceside.com/

OmniFlop
========
 - By Sherlock Consulting  (Jason Watton)
 - A 'universal' floppy disk reader, writer, and tester for the IBM PC or
   compatible which can handle alien floppy disk formats not normally
   supported by DOS, Windows and Linux.
 - OmniFlop on its own transfers disks between systems.  If you want to access
   files, for example, on these disks then you need more - you will need to
   use OmniFlop to image the disk, then other software to interpret the
   filing system.  OmniFlop alone only handles whole disks.
 - Features include:
    - Read, write, and format Atari 8-bit format (90KiB).  (Charles Doty)
 - First released in December 2004.
 - Runs under Windows 2000, Windows XP, Windows Vista and  Windows 7;
 - Earlier title OmniDisk runs under DOS and Windows 95 through to Windows Me
 - Available: http://www.shlock.co.uk/