Technically speaking, Snake Eyes and Storm Shadow are the closest of friends in all of the G.I. Joe Universe. They had some struggles in their past which caused them to be on opposite sides, but that was all cleared up long ago. Today (Figuratively speaking) they represent the closest allies in all of the comic universe.

The reason the two sword brothers are so often pitted against each other as toys and comic characters is for marketing. It is believed that Storm Shadow sells better as a "bad guy" toy, since it gives us two opposite-colored ninjas on opposite sides. In almost every alternate universe besides the Larry Hama-created "Canon" Mavrel series, Storm Shadow is portrayed as a Cobra for this reason.

In the original series, Storm Shadow and Snake Eyes only fought each other during two brief stints. The first was during the period where neither of them knew the other (issue #21) and the other was when Storm Shadow was captured by Cobra Commander towards the very end of the Marvel series, and brainwashed into doing the bidding of the evil Commander, along with Billy and the Baroness.