I have noticed while looking at early Mega Man X artwork that there has been a repeating pattern throughout several images. Alone, they mean nothing, but when you put them all together it makes you really wonder exactly just what it means. I am here to shed some light on this matter.
First off, take a good look at some pictures of X1. Namely, Armored Armadillo, Chill Penguin, and the cover art for the Japanese game. Do you notice something similar? I'll let it sink in... take a good, hard look... yeah, that's it. Their hands (with the cover art being Sigma in this case) have a very similar position. To describe it without looking at a picture, basically the middle and ring fingers are together while the index, pinky and thumb are spread apart. Now, this may just be a strange coincidence. Perhaps Inafune just wanted to do something interesting with their hands, rather than make them appear simply closed or left open? Well, I have more proof that this is far from a coincidence.
Take a look at look at Crystal Snail's picture from X2. You will notice that both of his hands are in the same position as well! Now, why would a character from a game made after X1 do such a thing? Also, take a look at the cover art for the Japanese version of X2--Serges' hand is also formed in a similar way. Do the similarities end here? Nope.
Next is X3. Toxic Seahorse's picture clearly has him showing off that marvelous hand sign in all of it's glory. Gravity Beetle, although it's not quite as obvious, has his hand positioned the same as the rest, too, although his fingers are bent.
X4 has a ton of references to the hand sign, although this time it is not in the art, but rather in the sprites. Double on the stage select screen has two poses where he utilizes the symbol... right in front of X's face (guess the blue bomber isn't the brightest bulb in the box). Sigma also uses it for his first form, with his palm turned upside down. Magma Dragoon uses at the end of his introduction pose as well. The strangest part is that members of the Repliforce use it as well: Frost Walrus uses it for his hurt poses and Slash Beast has his hands in that position for the ENTIRE fight! Lastly, X5 sees one person amongst the sprites to use the sign, Dynamo. For whatever reason his hand performs the gesture as he pulls his saber out. For the rest of the X5 and X6 bosses, however, no one ever uses it again.
Afterwards, the mysterious hand sign fades into obscurity, never to be shown again. So what was it's purpose? What was the meaning behind having so many characters use it, just for it to vanish at the drop of a hat? My one theory is that it was the symbol for the Mavericks, as a way in order to show their allegiance. As Sigma uses this himself in the series this is very likely and plausible, yet it begs the question as to why members of the Repliforce would bother using it along with Dynamo. An interesting thing to note is that the hand sign actually looks like a W in some forms--the same as the insignia used by Dr. Wily. It's logical to assume that it was meant to symbolize Wily's influence in the series, which lasted up until X6, the last game where the symbol appeared (although, this is only because they took Dynamo's sheet from X5 and reused it). If you were to turn it onto it's side, however, it also bears some resemblance the Greek letter for sigma, which could instead mean that it was used to show affiliation with Sigma himself, which could explain why Dynamo himself uses it, seeing as how he was affiliated with Sigma in X5!
Despite these possibilities, it still brings me back to the question why do members of the Repliforce use it? They are not actual Mavericks, they do not have any connections to Wily, and they are most definitely not affiliated with Sigma. Perhaps I am merely looking into the matter too hard, but it does seem odd that only two bosses out of a whole collection of other non-Maverick related bosses would use it. Maybe in the original planning stages Beast and Walrus had more to them than met the eye? Maybe they were originally going to be Mavericks, but somewhere during the development of the game they scrapped the idea? We all know that Walrus wasn't exactly the nicest boss in X4, and Beast certainly did have an attitude of his own to match. There are other Repliforce members that exhibit odd behaviors, such as Jet Stingray destroying an entire city, so perhpas, all in all, they really did become Maverick to a certain extent.
So what happened to it? Originally my guess was that it never caught on but with looking at X4 and X5 sprites, it makes me think that Capcom wasn't really striving for that. The most logical answer is that the Inafune leaving the series after X5 is the primary reason--after all, the last time the symbol was used was in X6, and that was only from sheer laziness on Capcom's part. Other than that... nothing. More than likely, though, if my bet on Wily being an influence for the symbol was correct, X6 was the last game that really needed to utilize it, seeing as how X7 and beyond completely removed any signs of the old doctor, much to fans disappointment. Even then, X5 was supposed to be the last game in the series anyway, since Wily had a huge involvement in the plot of that game, so it makes sense that the symbol was meant to end after that as X6 was never even supposed to EXIST. Still, even with Capcom completely messing things up, they oddly got such an obscure thing right. Funny how that works.
In all: Wily was the reason behind the hand sign. When Inafune left the X series as producer, the meaning behind the symbol was inevitably lost.