Here is a list of 3rd-party I-War missions I compiled a few years ago. It is followed by a list of sites where missions can be downloaded. Some of these sites no longer exist, but their content can be accessed in the Wayback Machine ( http://www.archive.org ).
3x1081.zip 3x10^8 vs Dreadnaught Designs
Chaos1.zip Chaos Gate
Chaos2.zip Chaos Legacy
Chaos3.zip Chaos Experiment
civ1_eng.zip Civilian 1: Grey and Orange
civ2_eng.zip Civilian 2: Journey to Xi Bootis
civ3_eng.zip Civilian 3: Sweet Julia
civ4_eng.zip Civilian 4: The other one's Game
civ5_eng.zip Civilian 5: The Name of the Game
civilian.zip Civilian (Mission Campaign)
cosam04.zip Cosa Mission 4 - "REPO Men"
cosamission2.zip "Peeping COSA"
cosamission3.zip "Destroyer Escort"
cosamission.zip Take Back What You Give - COSA Plays Nasty
dcosa1.zip (Take Back What You Give - COSA Plays Nasty for Defiance)
dcosa2.zip ("Peeping COSA" for Defiance)
dcosa3.zip ("Destroyer Escort" for Defiance)
demon.zip Demon Dimention
depotjob.zip The Depot Job
d_onebattle.zip "One Battle Sans Dreadnaught"
eato_1.zip
EATO_3.zip
EATO_4.zip
Howard.zip
How81.zip
Indie1.zip Indie1: The Amazon
Indie2.zip "Indie2: The Raid" v3.0
Indie3.zip "Indie3: A New Friend" v3.0
Indie5.zip "Indie5: RedEye Flint" (v1.0 Beta)
i-war_gaiden.zip i-war gaiden
M_Asteroids.zip "Asteroids"
M_IBattle.zip "Deep Space Infinite Battle"
mission65.zip Rejected Offerings
mission71.zip Going Underground: Part 1 New Millenium
MissionA.zip MissionA (based on Commonwealth Blackship "Spectre")
MissionB.zip MissionA (based on Commonwealth Blackship "Spectre")
Mosq1.zip Mosquito
m_VoyagerDuel.zip "Voyager Duel"
Phoenix1.zip Phoenix1 (based onboard the Phoenix, an independent PatCom)
Phoenix2.zip Phoenix2 (based onboard the Phoenix, an independent PatCom)
Phoenix3.zip Phoenix3 (based onboard the Phoenix, an independent PatCom)
Phoenix4.zip Phoenix4 (based onboard the Phoenix, an independent PatCom)
plane.zip "Fighter Duel" OR "Rip-Off: A Parady of Wing Commander"
proposal.zip (flying a spy ship for the Commonwealth)
rebel1.zip "Rebellion: New World Order"
rejected.zip Rejected Offerings (same as mission65.zip apparently)
Sal1.zip The Dark Salamanders
template.zip (template script)
Trinadyne.zip Trinadyne - Corporate Warfare (Mission One)
Voyagersoft.zip Voyager Duel (mod of a Nanoprobe mission)
vurt01.zip "And So It Begins"
http://www.i-war2.com/scripts.htm
civilian.zip Civilian (Mission Campaign)
depotjob.zip The Depot Job
mission65.zip Rejected Offerings
Phoenix1.zip Phoenix1 (based onboard the Phoenix, an independent PatCom)
Phoenix2.zip Phoenix2 (based onboard the Phoenix, an independent PatCom)
Phoenix3.zip Phoenix3 (based onboard the Phoenix, an independent PatCom)
Phoenix4.zip Phoenix4 (based onboard the Phoenix, an independent PatCom)
3x1081.zip 3x10^8 vs Dreadnaught Designs
civ1_eng.zip Civilian 1: Grey and Orange
civ2_eng.zip Civilian 2: Journey to Xi Bootis
civ3_eng.zip Civilian 3: Sweet Julia
civ4_eng.zip Civilian 4: The other one's Game
civ5_eng.zip Civilian 5: The Name of the Game
http://www.i-war2.com/scripts2.htm
cosamission.zip Take Back What You Give - COSA Plays Nasty
cosamission2.zip "Peeping COSA"
cosamission3.zip "Destroyer Escort"
cosam04.zip Cosa Mission 4 - "REPO Men"
d_onebattle.zip "One Battle Sans Dreadnaught"
M_Asteroids.zip "Asteroids"
M_IBattle.zip "Deep Space Infinite Battle"
MissionA.zip MissionA (based on Commonwealth Blackship "Spectre"
MissionB.zip MissionA (based on Commonwealth Blackship "Spectre"
http://www.i-war2.com/scripts3.htm
Sal1.zip The Dark Salamanders
Mosq1.zip Mosquito
m_VoyagerDuel.zip "Voyager Duel"
http://www.dreadnt.com/
Chaos1.zip Chaos Gate
Chaos2.zip Chaos Legacy
Chaos3.zip Chaos Experiment
Indie1.zip Indie1: The Amazon
Indie2.zip "Indie2: The Raid" v3.0
Indie3.zip "Indie3: A New Friend" v3.0
Indie5.zip "Indie5: RedEye Flint" (v1.0 Beta)
M_Asteroids.zip "Asteroids"
M_IBattle.zip "Deep Space Infinite Battle"
3x1081.zip 3x10^8 vs Dreadnaught Designs
mission65.zip Rejected Offerings
d_onebattle.zip "One Battle Sans Dreadnaught"
plane.zip "Fighter Duel" OR "Rip-Off: A Parady of Wing Commander"
eato_1.zip
EATO_3.zip
EATO_4.zip
proposal.zip (flying a spy ship for the Commonwealth)
demon.zip Demon Dimention
cosam04.zip Cosa Mission 4 - "REPO Men"
cosamission2.zip "Peeping COSA"
cosamission3.zip "Destroyer Escort"
cosamission.zip Take Back What You Give - COSA Plays Nasty
i-war_gaiden.zip i-war gaiden
Trinadyne.zip Trinadyne - Corporate Warfare (Mission One)
http://www.starshiprepulse.org/missions.html (Use Wayback Machine)
vurt01.zip "And So It Begins"
mission71.zip Going Underground: Part 1 New Millenium
Howard.zip
How81.zip
Chaos1.zip Chaos Gate
Chaos2.zip Chaos Legacy
Chaos3.zip Chaos Experiment
rebel1.zip "Rebellion: New World Order"
Indie1.zip Indie1: The Amazon
Indie2.zip "Indie2: The Raid" v3.0
Indie3.zip "Indie3: A New Friend" v3.0
Indie5.zip "Indie5: RedEye Flint" (v1.0 Beta)
MissionA.zip MissionA (based on Commonwealth Blackship "Spectre"
MissionB.zip MissionA (based on Commonwealth Blackship "Spectre"
Phoenix1.zip Phoenix1 (based onboard the Phoenix, an independent PatCom)
Phoenix2.zip Phoenix2 (based onboard the Phoenix, an independent PatCom)
Phoenix3.zip Phoenix3 (based onboard the Phoenix, an independent PatCom)
Phoenix4.zip Phoenix4 (based onboard the Phoenix, an independent PatCom)
Voyagersoft.zip Voyager Duel (mod of a Nanoprobe mission)
rejected.zip Rejected Offerings (same as mission65.zip apparently)
dcosa1.zip Take Back What You Give - COSA Plays Nasty
dcosa2.zip "Peeping COSA"
dcosa3.zip "Destroyer Escort"
Vader's Unseen Foe Mission:
http://www.remigianum.borken.de/schule/schueler/hooge/iwar/script.html (Use Wayback Machine)
Lost Missions:
[url=http://www.cc.jyu.fi/~juhkuus/I-War/missions.htm]http://www.cc.jyu.fi/~juhkuus/I-War/missions.htm[/url] (Use Wayback Machine)
Surprise: Introductions (by Brennen Guillory & Errol Pinto, description only)
[url=http://www.cc.jyu.fi/~juhkuus/I-War/missions.htm]http://www.cc.jyu.fi/~juhkuus/I-War/missions.htm[/url] (Use Wayback Machine)
Mission users may find Entropy's I-War Launcher to be of use. The original site is gone, but the site and downloads are still available through the Wayback Machine:
http://privat.schlund.de/e/entropy/iwarlaunch/readme.html

How do you download via the Internet archive? I can see the sites but none of the links work?

It looks like the download links on some of the sites don't work anymore (Starship Repulse, Vader's Unseen Foe), but the Lost Missions and Entropy I-War Launcher links do work for me. The Surprise: Introductions link has never worked as far as I am aware.
Sometimes the Internet Archive links don't work at a given time, but do work at a later time. I have also seen instances where functional links and pages in the Internet Archive seem to get mangled or disappear for no apparent reason. It isn't a particularly stable or robust system.