This is a little different the bibliography which is an awesome resource and lists all the Usagi Yojimbo stories.
What I have tried to do here is list all the comics, magazines, hardcovers and trade paperbacks that Usagi Yojimbo has appeared in, including alternative covers (which I generally hate but collect as I am a completest), or that Stan has contributed a story to. This does not include comics that just have a Usagi or Stan Sakai pin up. If anyone can confirm that this is correct or let me know if I am missing anything that I need to add that would be great.
Comics (354 different comics)
Usagi Yojimbo Summer Special (Fantagraphics Books, 1986) 1
Usagi Yojimbo v.1 (Fantagraphics Books, 1987) 1-38
Usagi Yojimbo v.1 Second Prints (Fantagraphics Books, 1987) 1, 10
Usagi Yojimbo v.2 (Mirage Publishing, 1993) 1-16
Usagi Yojimbo v.3 (Dark Horse Comics, 1996) 1-172
Usagi Yojimbo v.3 (Dark Horse Comics, 1996) - Variant Covers 123, 136
Usagi Yojimbo v.4 (IDW, 2019) 1-5 ongoing
Usagi Yojimbo v.4 Second Prints (IDW, 2019) 1
Usagi Yojimbo v.4 (IDW, 2019) - Variant Covers (24 for issue 1) 1 Daniel Warren Johnson 1:10 retailer incentive, 1 Walter Simonson 1:25 retailer incentive, 1 Kevin Eastman 1:50 retailer incentive, 1 AOD Collectables, 1 Brave New World, 1 Collector's Paradise/Knowhere Games, 1 Collector's Paradise/Knowhere Games virgin, 1 Comics & Ponies, 1 Comics & Ponies black and white lineart, 1 Dogu Chibi, 1 Excelsior Collectibles, 1 Frankie's Comics, 1 HeroesCon, 1 HeroesCon black and white, 1 IDW SDCC exclusive Sakai/Simonson virgin, 1 Incredible Con, 1 Jak's, 1 Legends Comics and Games Fresno, 1 New England Comics, 1 Other Realms, 1 Signing Tour/SDCC, 1 Sketch blank, 1 Slab City, 1 Vault Collectibles
2 IDW light blue logo
Usagi Yojimbo Color Special (Fantagraphics Books, 1989, 1991, 1992, DH 1997, 2014) 1-5
Usagi Yojimbo Color Special - Special Edition (Fantagraphics Books, 1989) 1
Albedo Anthropomorphics (volume 1) (Thoughts and Images, 1984) 2, 3, 4
Art of Usagi Yojimbo (Radio Comix, 1997, 1998) 1, 2
Critters (Fantagraphics Books, 1986) 1, 3, 6, 7, 10, 11, 14, 23, 38, 50
Darkhorse Maverick 2001 (Darkhorse 2001) 1
Darkhorse Presents v1 140
Darkhorse Presents v1 Annual (1999) 1
Darkhorse Presents v2 7 cover a, 7 cover b, 35, 36
Doomsday Squad v2 (Fantagraphics, 1986) 3
Drawing the Line (Drawing the Line, 2004) 5
More Fund Comics (Sky Dog Press, 2003) 1
Nocturnals: Troll Bridge (Oni Press, 2000) 1
Oni Double Feature (Oni Press, 2000) 11
Shell Shock (Mirage Press 1989) 1
Space Usagi v1 (Fantagraphics, 1992) ashcan, 1-3
Space Usagi v2 (Mirage, 1993) 1-3
Space Usagi v3 (Darkhorse, 1995) ashcan , 1-3
Star Wars: Jabba the Hut - The Betrayal (Darkhorse 1996) (contains a Preview Usagi) 1
Star Wars: Splinter of the Mind’s Eye (Darkhorse, 1995) (Preview Space Usagi) 1
Star Wars: The Clone Wars (2009 Free Comic Book Day release) 1
Teenage Mutant Ninja Turtles (Mirage Press, 1984) 47
The CBLDF Presents Liberty Annual 2014 (Image Comics, 2014) (3 covers) 1a, 1b, 1c
TMNT/Usagi Yojimbo (10 different covers) 1 Sakai, 1 Aragones, 1 RI Peterson, 1 Diamond Retailer, 1 Comics & Ponies /Kevin Eastman Fan Club, 1 Fried Pie Exclusive
TMNT/Usagi Yojimbo (10 different covers) Cont 1 Other Realms Exclusive, 1 SDCC Variant, 1 Sakai Signature Variant, 1 San Diego Comic Art Gallery Exclusive
TMNT/Usagi Yojimbo Samurai Special (came with SDCC 2017 action figure) 1
Trilogy Tour 2 (Cartoon Books, 1998) 1
Turtle Soup (Mirage Press, 1987) 1
Usagi Senso 1-6
Usagi Yojimbo Coloring Book (Usagi Studios, 2016) 1
Usagi Yojimbo Dojo 20th Anniversary Special (Usagi Yojimbo Dojo, 2016) (Ashcan limited to 150 copies) 1
Thirty-Fifth Anniversary Usagi Yojimbo Tribute Dojo Edition (Usagi Yojimbo Dojo, 2019) (Ashcan limited to 300 copies) 1
Usagi Yojimbo Sketchbook (Usagi Studios, 2004) 1-16
Usagi Yojimbo: One for One (specially priced #1 for $1 promotional reprint) Grasscutter Chaper 1 1
Usagi Yojimbo: One for One (specially priced #1 for $1 promotional reprint) Origin Tale 1
Magazines/Periodicals/Newspapers (23 different issues)
Amazing Heroes issue (1987 contains a Preview: Usagi Yojimbo) 112
Darkhorse Extra (promotional periodical - 1 page in each, 2000 and 2002) 20 21 22 23 45 46 47 48
Hawai'i Herald (newspaper with 8 page reprint story) (volume: 23) issue: 1 Friday, January 11, 2002
Previews (Diamond, 1996) 9 10 11 12
Previews (Diamond, 1997) 1 2 3 4 5 6 7 8
Wizard: The Comics Magazine 97
Hardcovers (59 different)
Usagi Yojimbo Books (Fantagraphics Books, 1990) (Darkhorse 1997) HC (limited) 1-33
Sakai Project: Artists Celebrate Thirty Years of “Usagi Yojimbo” (Dark Horse Comics, 2014) HC 1
Space Usagi Yojimbo Book (Darkhorse, 1998) HC 1
The Art of Usagi Yojimbo HC 1
Baltimore Comic-Con Yearbook 2013 1
Sixth Gun Vol. 4 Deluxe HC (Oni Press, 2017) 1
Sixth Gun Vol. 4 Gunslinger edition HC (limited 500) (Oni Press, 2017) 1
TMNT/Usagi Yojimbo (IDW, 2018) HC 1
TMNT/Usagi Yojimbo Expanded Edition (IDW, 2018) HC 1, 1 Signature Variant
Usagi Senso HC 1
Usagi Yojimbo Gallery Edition: Samurai and Other Stories (Dark Horse Comics, 2015) 1
Usagi Yojimbo Gallery Edition: The Artist and Other Stories (Dark Horse Comics, 2016) 1
Usagi Yojimbo Artist Edition: Grasscutter (IDW 2019) HC 1, 1 Dinner special (no bookplate, gold stamp instead)
Usagi Yojimbo Saga Omnibus Edition (Dark Horse Comics, 2014) HC 1-8
Usagi Yojimbo Saga Omnibus Edition Legends (Dark Horse Comics, 2018) HC 1
Usagi Yojimbo Special Edition - 2 volume omnibus in slipcase (Fantagraphics Books, 2010) HCs 1-2 (sold together)
Usagi Yojimbo: Yokai HC 1
Trade Paperbacks (49 not counting multiple printings) (Note every TPB except the MySpace and TMNT ones have HC versions)
Usagi Yojimbo Books (Fantagraphics Books, 1990) (Darkhorse 1997) TPB (multiple printings) 1-33
MySpace Darkhorse Presents TPB (originally web comics) 3, 6
Space Usagi Yojimbo Book (Darkhorse, 1998) TPB 1
The Art of Usagi Yojimbo TPB 1
Usagi Yojimbo Saga Omnibus Edition (Dark Horse Comics, 2014) TPB 1-8
Usagi Yojimbo Saga Omnibus Edition Legends (Dark Horse Comics, 2018) TPB 1
Usagi Yojimbo Special Edition 2 volume omnibus in slipcase (Fantagraphics Books, 2010) TPBs (multiple printings) 1-2 (sold together)
Usagi Yojimbo/Teenage Mutant Ninja Turtles: The Complete Collection TPB 1
Other Stan Sakai Comics
Nilson and Hermy books (not in same book as a Usagi story) (9 comics, 1 HC)
Albedo Anthropomorphics (volume 1) (Thoughts and Images, 1984) 1, 5
Critters (Fantagraphics Books, 1986) 5, 16, 27
Critters Special: The Adventures of Nilson Groundthumper and Hermy (Thoughts and Images, 1988) 1
Equine the Uncivilized (Graphxpress, 1989) 2 page cameo 6
Darkhorse Presents v2 30
The Adventures of Nilson Groundthumper and Hermy (Darkhorse, 2014) HC 1
47 Ronin (5 comics, 1 HC)
47 Ronin (Darkhorse, 2012) 1-5
47 Ronin (Darkhorse, 2014) HC 1
Misc (3 comics, 2 Magazines)
9-11: Artists Respond (many publishers, 2002) (Trip to NYC) 1
Amazing Heroes issue (1991, contains story explaining creative process) 187
Autobiographix (Darkhorse, 2003) (Trip to France) 1
Comics Journal Winter 2002 Special Edition (Shows a typical day in the office) 1
Darkhorse Maverick 2000 (Darkhorse, 2000) (Trip to Norway) 1
Role Playing Game (5 books)
Usagi Yojimbo Role Playing Game (Gold Rush Games, 1997) U100
Usagi Yojimbo Monsters RPG Sourcebook (Gold Rush Games, 2000) U101
Usagi Yojimbo Fantasy Role Playing Game (Sanguine Productions, 2005) 1
Usagi Yojimbo Fantasy Role Playing Game Limited Edition Release (Sanguine Productions, 2005) 1
Usagi Yojimbo Fantasy Character Design Book (Sanguine Productions, 2005) 1