Novels not in a series
Red Storm Rising (1986)
SSN (1996)

Jack Ryan/John Clark universe chronology

In the order in which they occur in the storyline (and when they occur):

Without Remorse (1970)
Patriot Games (1982, based on a reference to Ryan's age, which is 31 at the beginning of the novel. This roughly fits with a reference to the Princess of Wales's first child being a baby and a few months old, Prince William was born in 1982) Discrepancies include the reference to a van having a likely year of manufacture of 1984.
Red Rabbit (circa spring of 1982, based on references to living Leonid Brezhnev and Mikhail Suslov, both of whom died in 1982, as well as Jack Ryan, Jr.'s age in the novel, 6 months) Discrepancies with the estimate of 1982 include frequent references to "Transformers" which did not appear until 1984 and the fact that the Orioles played the Phillies in the World Series in 1983, not to mention that the World Series is played in the Fall, not the Spring. Also a reference to "Coke Classic" which did not debut until the summer of 1985.
The Hunt for Red October (1984)
The Cardinal of the Kremlin (1986) – "The first chapter is set in January and states that Ryan is 35 years old. It also has references to the other books set earlier. For example the Foleys have been in Moscow for almost four years. The book must begin (not including prologue which was set end of previous year) in January 1986.

Starting with the following novel, the series becomes distinctly different from real history as noted below.

Clear and Present Danger (1988) The book refers to Jack's age at 40.
The Sum of All Fears (1990–1991) — Israel partially cedes sovereignty over Jerusalem to the Vatican and Saudi Arabia, and the city becomes a United Nations protectorate policed by Swiss Guards. Residents of Jerusalem can choose between either Vatican, Israeli or Islamic judicial law. Denver is devastated by a terrorist nuclear explosion. The book occurs after the Persian Gulf War and before the dissolution of the Soviet Union. It is implied that both events occur at the same time in the Ryan universe as in actual history (of the Soviet Union dissolution), 1991. In the earlier chapters it states that it had almost been two Novembers since President Fowler had been elected, making the beginning set in 1990. Interestingly, the video game Tom Clancy's Rainbow Six puts the atomic detonation in Denver as having occurred in 1989.
Debt of Honor (1995–1996) — The U.S. and Russia destroy all of their ballistic missiles. After crippling the U.S. economy and becoming a nuclear power, Japan invades and takes the Marianas Islands; the United States and Japan fight a brief war, which the Japanese lose (they are subsequently denuclearized); an embittered Japanese pilot and proponent of the war crashes a 747 into the United States Capitol Building immediately after Ryan's confirmation vote for the Vice President, killing most of the House and Senate, the President, all nine Supreme Court justices, the senior military establishment (including the JCS), and most of the Cabinet; Ryan is left in charge of a gutted government. The end of the book occurs eleven months before 1997 presidential inauguration. Of interest, but not crucial to the plot of this or further books is that North and South Korea were said to be unified at some point between The Sum of All Fears and this book.
Executive Orders (1996) — Saddam Hussein is assassinated; Iran and Iraq merge forming the United Islamic Republic; the UIR launches a biological attack on the U.S. using the Ebola virus; the United States launches the Second Persian Gulf War against the UIR and defeats them; the Ayatollah is killed in a smart-bomb attack by the U.S.
Rainbow Six (Takes place between Executive Orders and The Bear and the Dragon most likely 1998-1999 from a statement saying that it had been a year and a half since Jack became president and the date of the video game) (although events seem to be based on the Sydney Olympics held in 2000) RAINBOW — an elite counter-terrorist force — is created and engages terrorists across Europe. Ecoterrorists plan to create a genetically-enhanced virus based on Ebola and cancer cells, which they plan to use to wipe out much of the world's population.
The Bear and the Dragon (2000) — Russia is admitted to NATO; China and Russia fight a major war, in which the U.S. intervenes on its NATO ally's side. It implies that the British Prime Minister is Tony Blair.
The Teeth of the Tiger (2005, based on the age of Jack Ryan, Jr.) The U.S. is now engaged in a global war on terrorism, in response to the September 11 attacks, which occurred in the Ryan universe as they did in the real world. It is mentioned that the wars in Afghanistan and Iraq occurred in the Ryan universe continuity, and that the Jerusalem Treaty signed in The Sum of All Fears has failed as Israelis and Palestinians went back to fighting each other.
Dead or Alive (2010, based on Jack Ryan's announcement that he would run against Ed Kealty for President "in the coming year") — The Umayyad Revolutionary Council (the Ryan universe version of Al-Qaeda) and its leader "The Emir" (based on Osama bin Laden) plan a string of major attacks on the U.S. The wars in Afghanistan and Iraq continue, as in our timeline, and President Kealty is in the process of withdrawing U.S. troops from Iraq, a process that began in our timeline in 2009. A character also explicitly refers to the date as May 2010, in the process of decoding encrypted messages.
Locked On (2011, based on Jack Ryan Sr.'s campaign for re-election). During the 2012 US Presidential Campaign (Election Day is specifically mentionned as the 6th of November, a Tuesday), Jack Ryan Sr.'s opponent, Edward Kealty, tries to dig up dirt on him by going after John Clark. Meanwhile, a renegade Pakistani general steals nuclear weapons from his country and delivers them to rebel Dagestani forces. In the middle of all this, Jack Ryan Jr. and The Campus try to prevent the use of the lethal weapon and come to help Clark.
Threat Vector (2012)
Command Authority (2013)

Op-Center universe

Op-Center (1995)
Mirror Image (1995)
Games of State (1996)
Acts of War (1996)
Balance of Power (1998)
State of Siege (1999)
Divide and Conquer (2000)
Line of Control (2001)
Mission of Honor (2002)
Sea of Fire (2003)
Call to Treason (2004)
War of Eagles (2005)

Net Force universe

[b]Net Force (1999)
Hidden Agendas (1999)
Night Moves (1999)
Breaking Point (2000)
Point of Impact (2001)
CyberNation (2001)
State of War (2003)
Changing of the Guard (2003)
Springboard (2005)
The Archimedes Effect (2006)

Net Force Explorers universe

Virtual Vandals (1998)
The Deadliest Game (1999)
One is the Loneliest Number (1999)
The Ultimate Escape (1999)
End Game (1999)
Cyberspy (1999)
The Great Race (2000)
Shadow of Honor (2000)
Private Lives (2000)
Safe House (2000)
GamePrey (2000)
Duel Identity (2000)
Deathworld (2001)
High Wire (2001)
Cold Case (2001)
Runaways (2001)
Cloak and Dagger (2002)
Death Match (2002)

Power Plays series

Politika (novel, 1997)
ruthless.com (novel, 1998)
Shadow Watch (novel, 1999) by Jerome Preisler
Bio-Strike (novel, 2000) by Jerome Preisler
Cold War (novel, 2001) by Jerome Preisler
Cutting Edge (novel, 2002) by Jerome Preisler
Zero Hour (novel, 2003) by Jerome Preisler
Wild Card (novel, 2004) by Jerome Preisler

Ghost Recon universe

Tom Clancy's Ghost Recon by Grant Blackwood as David Michaels
Tom Clancy's Ghost Recon: Combat Ops by David Michaels

EndWar universe

Tom Clancy's EndWar by Grant Blackwood as David Michaels
Tom Clancy's EndWar: The Hunted by Grant Blackwood as David Michaels

H.A.W.X universe

Tom Clancy's H.A.W.X by Grant Blackwood as David Michaels

Non-fiction

Guided Tour

Submarine: A Guided Tour Inside a Nuclear Warship (1993)
Armored Cav: A Guided Tour of an Armored Cavalry Regiment (1994)
Fighter Wing: A Guided Tour of an Air Force Combat Wing (1995)
Marine: A Guided Tour of a Marine Expeditionary Unit (1996)
Airborne: A Guided Tour of an Airborne Task Force (1997, ISBN 0-425-15770-9)
Carrier: A Guided Tour of an Aircraft Carrier (1999)
Special Forces: A Guided Tour of U.S. Army Special Forces (2001)

Study in Command

Into the Storm – On the Ground in Iraq (with Fred Franks) (1997)
Every Man a Tiger — the Gulf War Air Campaign (with Chuck Horner) (1999)
Shadow Warriors — Inside the Special Forces (with Carl Stiner) (2002)
Battle Ready (with Anthony Zinni) (2004)