One interesting thing to note about Usagi Yojimbo is that for many fans - their first exposure to the Samurai Rabbit came from Teenage Mutant Ninja Turtles.
You see, Peter Laird and Stan Sakai were friends -- and their respective characters launched around the same time. This self portrait of the two illustrates their friendship, and occasional crossover with their characters.
The first cross-over between the characters occurred in Usagi Yojimbo #10 (Volume 1). It was a short back up tale - and featured Leonardo and Usagi crossing paths, and teaching Usagi a lesson about respecting everyone.
Usagi made his transition to television for the first time in the original TMNT TV series. Two episodes guest starred the rabbit - though they mistakenly named him "Usagi Yojimbo", instead of his real name as "Miyamoto Usagi". Outside of independent comic fans, his appearance here was probably what made most people aware that Usagi Yojimbo existed. He even received two action figures (a normal one, and a Space Usagi toy) - both with wildly different interpretations of what Usagi really looked like. The regular Usagi figure was apparently one of the most sought after characters (besides the Turtles themselves) on store shelves!
The next cross-over between Miyamoto Usagi occurred in his newly rebooted second volume, with a three-part storyline. (These issues where in color, at the time; though reprints of this story, in Volume 8 "Shades of Death", the story is in black and white)
Usagi and his bounty hunter friend Gen, becomes engaged in protecting a wizard from the Neko Clan of Ninja. Note; the wizard looks conspicuously like Splinter! Fearing that two Samurai would not be enough to protect him and the village he lives in, baby Turtles are brought to him -- which the Wizard uses to summon...
...The Teenage Mutant Ninja Turtles!
Not just Leonardo, but the whole group appear in Usagi's world. The brothers are amazed in be in ancient Japan - though confused as to why everyone are anthropomorphic animals. Leonardo is at least able to vouch for Usagi.
So the Turtles help protect the wizard, defeating the Neko Clan Ninja's ambitions, and eventually returning home. It was a wonderful 3-part story; and I hope helped bolster Usagi's name to new readers through use of the popular Turtles.
In 2003, Peter Laird helped develop a new, more serious, Teenage Mutant Ninja Turtles show -- which, like in the late 80s and early 90s, would once again feature Usagi Yojimbo as a guest star. This time, however, Usagi would be in a much more serious storyline than from his appearance in the old cartoon show.
Traveling to another world, the Turtles are exposed to the Multiversal "Battle Nexus Championship". In a spectacular 4-part episode, we're shown how the Battle Nexus Championship brings people from all across the multiverse to participate in a grand battle of skill and honor. Evil trappings are afoot, though, as the Turtles become embroiled in an attempt to take over the Championship. This is where Leonardo and Usagi Yojimbo meet, helping each other foil the plot of the villains.
This depiction of Usagi was simply done perfectly! Gen likewise guest starred in the episode, further fleshing out Usagi's own world to new fans.
The Turtles and Usagi would meet again, though, when the villains from the Championship return - sending the 4 Ninja Turtles across the Multiverse! Leonardo lands in Usagi's world -- and we are treated to an awe-inspiring actual episode based in Usagi's world.
Characters like Tomoe, Lord Noriyuki, and the evil Lord Hebi are featured. Its even noted that Ninja, (like real Ninja in history) are usually not to be trusted; Ninja and Samurai are like oil and water.
During the course of the 4th season of the 2000 Ninja Turtles series, Leonardo faces a harsh blow from the Shredder - which leaves him in an emotional tailspin. Sensing his son needs the help of a friend, Splinter uses the Battle Nexus Tournament gateway to recruit Usagi - and bring him to the modern world. Its a fun episode - showing Usagi and Gen seeing a world they could never have imagined.
They even make use of Gen, a Rhino, and dress him up like Rocksteady from the old cartoon! Sadly, Usagi's visit wasn't enough to bring Leonardo out of the depression.
Plans where made, during TMNT: Fast Forward series, to have a cross over with Space Usagi (a future version of Usagi Yojimbo). Since Fast Forward didn't continue further, those plans went undeveloped.
That was the last time TMNT and Usagi Yojimbo crossed over. I sure hope it isn't the last! Stan Sakai has been asked wether Usagi might appear in the new Nickelodeon TV series - but it sounds like there would be issues with contracts, and it simply isn't a possibility.
It is worth noting, though, that the recent TMNT movie featured a small reference to Usagi Yojimbo. When mentioning the drug trails, the Turtles where experimented on, it was referenced that bunnies where first used (in reference to the close date Usagi appeared in comics, shortly before TMNT debuted.)