I'm not a huge fan of the ninja boys. Not to say I don't like them, I just don't get hung up in their story, I prefer the conventional ground pounding, trigger pulling troops. Same with SW, could care less about the Jedi/Sith, more into Wedge and Rogue/Wraith Squadrons.
Boba Fett is my favorite SW baddie, and my fave Joe baddie is the Fett of the Joe-verse: Fire Fly. Been reading more and more about him, dude is just a bad-ass.

I've got the VvV Snake Eyes that came with Swamp Rat, and besides the fact that he can't seem to stand up on his own, he seems to be a good sculpt of the figure. In this example, he seems to be more "commando" and less "ninja." The only Storm Shadow I have is Tommy from Viet Nam, not really the epitome of the character, so I'm thinking of getting a Storm Shadow just to have him.

Seenings how there is somewhere around 2,957 versions of Snake and Storm, what do you fine folks consider the best example of each of these characters?

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There was a big chunk of time, where I just wasn't paying attention to toys. So, when I think of Snake Eyes, I think of his V2 version. I also really like the commando look of the original. The 25th incarnations of those two looks, are the only Snake Eyes(es?) in my collection. I can't really decide which is my defacto Snakes.

Like you, I'm not a huge fan of ninjas. (still don't know why I made that Jinx) I only wanted a Storm Shadow, because he seemed like such a central Cobra character, in the cartoons. The only version of him I own is the one from the Cobra five pack, from the end of the 25th line. I want to make him a new backpack, with no quiver, just the sword sheaths.

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I'm not a huge Snake-Eyes/Storm Shadow fan, but I can respect their place in the mythology. Plus they're the "Face" of the franchise so as an unofficial ambassador of Joe, I always have to pretend they're my favorites when I'm talking to kids in the toy aisle or Cub Scouts

As for favorite versions, that's a toughy. I prefer my Snake-Eyes more "ninja-ey" than most adult Joe fans because I find the straight commando gig boring. I also prefer Tommy have a bit more to him than a plain white ninja.

As a kid Snakes V3 and Stormy V2 were the only versions I ever had so I still have a fondness for them, though Storm Shadow is and always will be a Cobra to me. V1 of both characters were great figures too, simple but effective designs. So the 25th (Vastly superior to the originals) versions of those will always rank high on my list even though they run contrary to what I wrote above

I never saw a V2 Snake-Eyes until I was an adult, and when I finally looked at the figure, I realized just how horrible it is. Chubby and dumpy with a feminine face and footy pajamas. There is not one single part of that figure I like. Even the 25th update which fixed a lot of this figures major problems didn't do much for me and then they just keep redesigning it closer to the crappy ARAH versioon. So V2 is way down at the bottom of my list.

OK, so enough lead in, what are my absolute favorites?

Snake-Eyes: Target exclusive ROC w/Ninja cycle. This figure has got everything I want in a Snake-Eyes. It's got a little color, it's got a splash of black, it's got a healthy dose of ninja elements, it's got plenty of commando bits, it's got a touch of the classic Snake-Eyes, and it's got a bit of the movie version too.

I love this figure. The only problem I have with it is getting it away from my boys because they love it too.

Storm Shadow: I'm going to cheat a little here and vote for the Pursuit Of Cobra Jungle Strike Storm Shadow. Yeah he's not out yet, but I've seen it up close enough to know that I'm in love.

I'm not a huge fan of Resolute's character designs (KNEEPADS FOR EVERYBODY!!!) but I like the Storm Shadow mold. I also like that the figure is not plain white or white with tetris grey camo. It also wins for all the reasons my Snake-Eyes does. It touches on a little of everything the character is, was, and will be and combines it into a solid figure.

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My overall favorites of each character are the NS Snake-Eyes (packed w/Swamp Rat) and 25A Hall of Heroes Storm Shadow.

To break it down by type, though:

ARAH:

'82/'83 Snake-Eyes. The later versions seemed too over-the-top for me. The last version might have been okay, but the blue ruined it for me.
'84 Storm Shadow. The following versions were good too, but the first one set the bar mighty high.

NS:

See above for Snake-Eyes.
Mail-in Storm Shadow. The body mold had already seen several uses, but the mostly white (unpainted Dragon detailing) actually made the design more interesting. The Tommy head sculpt was a nice treat as well.

25A:

Body Damage Snake-Eyes. Sooooo many Snake-Eyes, but this one is still in dark colors (charcoal grey with black gear) and has damaged uniform parts to make it stand out from the rest.
See above for Storm Shadow.