From the A8FAQ...  ( https://www.atari800xl.eu/faq/atari-8bit-faq.txt )

Subject: 8.11) What programs use a computer mouse?

Programs that use the Atari Mouse (STM1/PCM1) or compatible (which would
include the Zobian Controls SuperRAT):
- 8Bit-Mouse (BPAUG)
- Accu-Draw, by Vision software for Zobian Controls, 1987
- Artprog
- Atari Rechner Simulation mit UPN, (c)1985 MTC Mouse Tecnology Corp.
- Black Magic Composer by Sven Tegethoff for Ulf Petersen, 1991
- Bomb Down by The Roemer/U.N.O.
- BOSS-X by Mirko Sobe / MS Software, 2003
- The Brundles by KE-Soft, 1993 (hold SPACE at boot for configuration)
- The Brundles Editor by KE-Soft, 1994
- CardStax 2.1 by David A. Paterson, 1993
- Catch 88 by Simon Trew, 1991
  - Supports Multi-Mouse ST Mouse Driver by Simon Trew
- Celebrity Cookbook by David Sullivan/Total Control Systems for U.S.A. Media
- Click! by Chris Martin, 2008
- Contiki OS package for Atari, by Oliver Schmidt
- Copy F'n'F by Mirko Sobe / MS Software, requires BOSS-X
- Crescent Solitaire, Zdenek Eisenhammer, Frantisek Houra, Marek Pesout, 2018
- Datenbank by Mirko Sobe / MS Software, requires BOSS-X
- Diamond GOS by Reeve Software
- Diamond Develop by Reeve Software, requires Diamond GOS
- Diamond News Station by Reeve Software, requires Diamond GOS
- Diamond Paint by Reeve Software, requires Diamond GOS
- Diamond Write by Reeve Software, requires Diamond GOS
- Enigmatix! by Stephen A. Firth for Page 6, 1993
- EORoid by Daniel Kolakowski for Wolf Software Ltd, 1994
- Facher Patience, by Kemal Ezcan for Zong 1/93
   - with KE-Maus Beispielprogram
- Fig-Forth by Matt Symonds for Pulsar Software, 1988
- FireBall (a Breakout game, requires SAM)
- GOE demo by Total Control Systems/David Sullivan, 1988 
- Guntris by Richard Gore, 1996
- Hardwaretester/Peripheral Test 2.0 by Florian Dingler, 2008
- Hong Kong, Kemal Ezcan for Zong 5/93
- Klony 2010 by Arkadiusz Lubaszka for ArSoft, 2010
- Knight Quest by Simon Trew, 1991
  - Supports Multi-Mouse ST Mouse Driver by Simon Trew
- Kriss Kross by Simon Trew, 1992
  - Supports Multi-Mouse ST Mouse Driver by Simon Trew
- Macao, by Alexander Klinner for Zong 5/94
- Mau Mau X by Mirko Sobe / MS Software, requires BOSS-X
- Maus Calculator, by AMC Verlag, (c) by Peter Eilert
- Maus-DOS, by Volker Matzat for Zong 5/93
- Minesweeper by Harald Schoenfeld for PPP, 1992
- Mine Sweeper by Raindorf Soft
- Mine Sweeper 3
- Missile Command by Rob Zdybel for Atari, 1981.  [CONTROL+T] for trackball/
  mouse mode, according to Atari's 1987 documentation supplied with the XE
  game system (with Missile Command built-in).  In fact, the game's
  (originally undocumented) trackball mode inadvertently also supports many,
  but not all, versions of the Atari STM1/PCM1 and compatible mouse.
- M.O.S. (from Abbuc mag.)
- MS-Copy 1.1 by Mirko Sobe / MS Software, requires BOSS-X
- Multi-Mouse ST Mouse Driver by Simon Trew for New Atari User #42 1990
- Multi-Player by Madteam
- Multi-DOS
- Numblines by Jaroslaw Kucisz & Tomasz Kucisz for Utopia Software, 1997
- Operation Blood, P. Kalinowski & P. Bulkowski of Our 5oft for Mirage and
  ANG, 1992
- Othello by Simon Trew, 1991
  - Supports Multi-Mouse ST Mouse Driver by Simon Trew
- P-Graph(s) by ??? 
- Pad 1.2 (Padnoid) by Nelson Ramirez / New Age, 1995
- Pad 1.83 by Nelson Ramirez, 2014
- PLATOTerm by Thomas Cherryhomes, 2018
- QUICK Ed Character Editor by PPP
- RAOS Desktop, by Syntel for Zobian Controls, 1987
- SAM (Screen Aided Management) by Power Per Post & Raindorf Soft (a GUI!)
- SAM Budget (80 column spreadsheet program, requires SAM)
- SAM Convert (text files to/from the SAM Texter format, requires SAM)
- SAM Creator (SAM Painter files to/from Micro-Painter format, requires SAM)
- SAM Designer (drawing and design / desktop publishing, requires SAM) 
- SAM Memobox (card filing program, requires SAM)
- SAM Monitor (view and change memory, requires SAM)
- SAM Painter (128 color paint program, requires SAM)
- SAM Texter (80 column word processor, requires SAM)
- Screens 2.0, by Zobian Controls, 1987
- Shanghai by Peter Sabath for Activision, 1987
- Special Forces (Operation Blood II), P. Kalinowski & P. Bulkowski of
  Our 5oft for Mirage and ANG, 1993
- Sprint XL (from Abbuc)
- Tommingi by Tomek Borygo
- Toy'Swap by Victor Parada, 2015
- TRS Desktop by Tristesse, 2006
- Unriagh II by Uwe Hartwig, 1986
- Vanish, Kemal Ezcan for Zong 7/93
- Vier gewinnt 
- See also Fandal site search for games that use the Atari mouse:
  http://a8.fandal.cz/search.php?search=mouse&butt_details_x=x
- See also AtariMania lists of games & utilities using the Atari mouse:
  http://preview.tinyurl.com/mcm6wwo
  http://preview.tinyurl.com/oa7gklk

Programs that could use the original Zobian Controls RAT 
(which never shipped?):
- Accu-Draw (Rat Trace), by Vision software for Zobian Controls
  (original version for original RAT; never shipped?)
- Business Manager by Reeve Software, 1986
- Control (Rat Control) by Zobian Controls (never shipped?)
- Master Disk Directory II by Zobian Controls (never shipped?)
   - Based on Master Disk Directory by Jason Leigh, Analog #37 Dec85 p99-108
- Rich Man's Word Processor, by Mark Rogalski for Computer Software Services
   - Earlier name: Writer80
- Also announced by Zobian Controls in RAT-compatible versions (never 
  shipped): Super 3-D Plotter (Elfin Magic), Rambrandt, 
            Atari-Artist (AtariArtist)

Programs that use the Amiga mouse (original "tank" or 1352 models):
- Black Magic Composer by Sven Tegethoff for Ulf Petersen, 1991
- Bomb Down by The Roemer/U.N.O.
- Contiki OS package for Atari, by Oliver Schmidt
- Crescent Solitaire, Zdenek Eisenhammer, Frantisek Houra, Marek Pesout, 2018
- Global War by P.M.M. Elfinger & D.J. Garbowski for L.K. Avalon, 1993
- Klony 2010 by Arkadiusz Lubaszka for ArSoft, 2010
- Multi-Player by MadTeam 
- Najemnik - Powrot by LK APM for Krysal Software
- Operation Blood, P. Kalinowski & P. Bulkowski of Our 5oft for Mirage and
  ANG, 1992
- Pad 1.83 by Nelson Ramirez, 2014
- PLATOTerm by Thomas Cherryhomes, 2018
- Samurai's Game by Rafaell Soft for Krysal Software, 1992
- Special Forces (Operation Blood II), P. Kalinowski & P. Bulkowski of
  Our 5oft for Mirage and ANG, 1993
- TRS Desktop by Tristesse, 2006
- See also Fandal site search for games that use the Amiga mouse:
  http://a8.fandal.cz/search.php?search=amiga+mouse&butt_details_x=x

Programs that use the Commodore 1351 mouse (mouse for Commodore 64/128):
- Klony by ArSoft, 2006

------------------------------

Subject: 8.12) What programs use Driving Controllers?

Programs that use the Atari CX20 Driving Controller:
- Megaoids by Peter J. Meyer and Lance Ringquist for Video 61, 2016
- Tempest Elite by Peter J. Meyer for Video 61, 2017
- Tile Smashers by Peter J. Meyer for Video 61, 2017