[Snowflakian]

It can vary.
One of the best things about the starwars crossover is the death star itself. How many lines really have things of that epic that could work?

Marvel only 'works' as is for now because of the idea of the marvel scientists getting ahold of classic G1 tech. Reed, and tony, forge, and so on. But it'd be nicer if they went more accurate vehicles from within the mythos. Which were also joe scale compatible. Like 4 pieces of the fantasticar, ghostrider's bike, or just more accurate vehicles like blade's car. The Venom Crossover works in this regard as it's like a symbiote possessing Downshift.

But even on a subtler route, why not a GI Joe off shoot like inhumanoids was?
You could then have a crossover of figures with various aesthetics, from joe to inhumanoids, to centurions, and even a silverhawks space program...

Some anime could work, but it's best to blend the lines that are most compatible.
Like the 2012 upcoming bubblegum crisis movie if it stays on time. Why not let hasbro get the rights to it, and other kenichi sonada works for Joe scale rally vincent, bean bandit, TF crossovers bean bandit car, Bubblegum crisis armors and bikes classic, 90s, and movie. The bridge gaps that allows with the various 'boomers' could even tie to allspark energy. You could cross mikayla into something like that easily. TF Animated Sari proved it popular when done right, whereas Transformers Energon only kinda made it annoying. That was one of the golden things about the 80s. The shows loose ties to each other.
Transformers and Joes intermingled character wise, and references, then joe and inhumanoids, among others. It was one giant net weaved world.

But mostly it's just the scale like crossover that works the best. Not always blatant like transformers ones, we've also seen such a rise in the likes of joe scale usage, from marvel, to terminator, and even ben 10 and motion revive series.
Like the joe scale marvel figures, oh wouldn't I give for joe scale anime icons.
Like ryoko in battle armor, Ryo Ohki mech with sasami, pretty sammy, pretty cure, garo, and others of that ilk, Tenchi in love tenchi masaki in ninja armor, soul and maka, lupin, etc. Besides of course the first 90s Bubblegum crisis armors.
Plus the Ryo Ohki mech can work for plushes and transformering, also stuff like FLCL would work.

Power Rangers and Kamen rider have dabbled in this foray too. Albeit limited success, the japanese toku genre has mastered it pretty well. Looking at Faiz, and decade respectively. Bandai's motion revive also perfected this if they hadn't stopped making riders right before decade.
Though their american attempts have been rather gawdy. That's the one thing to remember, and why SW transformers survive. Accuracy to both a SW character, and a vehicle.
Thankfull something like Bubbgle gum crisis makes this easier with what vehicles are presented, and why not the AD Police guy into his car?

This would really only work well for the overtly capable lines. Stuff like dragonball and naruto, or bleach wouldn't really fit, whereas stuff like soul eater with it's whackiness(SQUARE FTW! SOUL EATERxKINGDOM HEARTS someday?!) or other icons like astroboy or megaman could still work. And who wouldn't want Joe scale kingdom hearts figures? Or Soul Eater ones?

Video game characters could really expand the idea somewhat too. Masterchief in joe scale or turns into vehicles? Sure why not. Capcom characters? Konami? Tecmo, so many could work in joe scale, but only a few like Metal gear solid, viewtiful joe, megaman, and Xenosaga could work in transformers. Burning Rangers is another that could play to both.

Accuracy and capabilities are the key. I would outright buy human alliance michael knight and kitt (with web animation hyper mode robot mode). And Barbie seems to do some crossovers not bad either.

But I don't see the logic in making naruto become a shuriken or vehicle. But Naruto to fox cold work like old school digimon figures. And while yes soul eater to weapons is obvious, but why not also the powered up forms, or simply the whackiness that is Shinigami's robot. Or Maka as the hybrid human weapon awesomeness. Not really transforming but they do use the same principle as automorph and mech alive.

And I won't even bother with the awesomeness, of robotech, exosquad, voltron, macron 3, and more that could benefit. Or SerpentO.R. that turns into a chariot for joe serpentor to ride. Or the Ghost in the Shell spider tanks.

Kingdom hearts seems to be the best approach to this methodology for some worlds.
But media relating it, if even just a one shot special, would help carry them better. That's one of the reasons Kingdom hearts does it well. It just has to have a moderate amount of sense to the presented line, and be cool without becoming a roleplay weapon. No kid wants an ironman axe, or spiderman gun. Thor is probably the only exception to this. But thors hammer is also the name of a military weapon too.

So I guess my final vote is, Accuracy to vehicles is a must for intended purposes to kids. For joe scale it has to be accurate and or just aestheticly pleasing with a wide array of choices, Inhumanoids for example can do this and bridge 3 gaps easily of marvel, joe, and transformers. If the joe scale were to dabble in anime, it'd have to be the surreal or similiar as well.
Bubblegum crisis, Ghost In the Shell, Soul Eater, Trigun, Devil may Cry, Tenchi Muyo, Kingdom hearts, capcom and metal gear solid. Even Samus, and Link, or Mecha Sonic. (Robotnik roboticize!)
Most of these would be ripe to go joescale or transformers.

Besides, who doesn't want Movie GI Joes, using Movie transformers as vehicles? Scarlet with Flareup and a third powered armor mode for reverse pretendering. Or snake eyes, or baroness for that matter. Best of BGC, Transformers, and Joe all in one off shoot line. That could become a new inhumanoids sari/mikayla allspark hunting thing. >.>
Sari in Joe Scale, Mikayla as a movie stylized version of Sari in joe scale, nest, GI Joe, earthcorp, Mask, and so on all being secret organizations like stargate only with allspark tech? Again why not. Then each can have subgroups or 'prototype' armors. Like more loosely based on Sari/Movie stylized Sari/BGC besides just the various inhumanoid monstrous armors, or the joes accel armors, or the reactive armors, or even maskes helmeted plain clothes decon like suits. =D The new weapon X initiative being hired by cobra. Etc.

Of Course then again, I could be biased since I've already made 2 GI joe reactive armor X-23s. And use a Cobra combined with shocker logo for my sig...

That's another that could be amazing to see. Cobra and Shocker merging for one massive genetic supersoldier army nightmare inspired by the red skull, Making GI joe unite with ambassadors like kamen rider 01, 02, and v3, black panther, storm, captain britain and union jack, canada's hero Guardian, captain america, etc. You just have to be selective with the icons and how it's presented.

Marvel VS Capcom, SNK vs capcom chaos, NamcoXKonami, Super robot wars OG saga endless frontier, Kingdom hearts, all of these video games worked as crossovers. And would be perfect for Joe scale figures as well. To mix by that same notion they each use to present it. They could even work for TF crossovers.

Fringe, Sliders, X-files, Reboot, soul eater, tenchi muyo, the gunsmith cats, Knight Rider and others all work for visual gag crossovers at least. That becomes an interesting question when you put references from all over instead of selective ones.
TFA experimented with this on the multiverse like level of it's own characters. Just as the tenchi muyo creator has a tenchi reference in his works. Then we have shows like robot chicken that just use them all. Could a serious show work like that? Maybe. It'd throw people a big enough curve ball while being nostalgic. Like what if megatron tech helped make some of the mechanical stuff, and extreme quantum science stuff. Or what if Jem appeared on heroes as an Idol who could project holograms around herself as a power, and cashed in on the money of her pop star status, and anonymity? Somethings are intrigueing while others are lame, I guess navigating the waters is kinda hard.

Even tron is just begging for joe scale figures, AND TF crossovers ones.
oh and 5 more words.
Cloverfield as an inhumanoids prequel.