Reichu: Seele's crest is also found on Lilith's mask for reasons that probably won't ever become clear.
Keisuke-kun: The seven eyes are probably a reference to the “seven eyes of God,” mentioned twice (without much to it) in the Bible (Zechariah3:9 and Revelations5:6). “Eyes of God” in general are mentioned in the Bible a multitude of times.
thewayneiac: It's also been pointed out that if you add up the number of eyes on the first three Evas, you get seven. (1 + 2 + 4 = 7) I've never been sure if this actually means anything, though.
Reichu: The shape of the triangle has become associated with God, partly because He encompasses a Trinity: Father, Son, Holy Spirit. (Robert Fludd — mentioned back in 002b — also depicted God as a triangle in his works.) The fact that the triangle in Seele's mark is divided in half also gives us a second ‘trinity’, of sorts, in that it creates three triangles (the two halves and the whole). In any case, Seele chose their symbol aptly, considering they're an organization out to evolve humanity into something equivalent to God. Or reunite it with God. Or something.
HeWhoPostsStuff: The pretty rainbow colors always looked weird on that ominous logo, in my opinion. Perhaps a passing reference to the rainbow which God put up in the sky after Noah's flood, as a promise that he would never repeat such an event? Probably not … I'd say it's more likely that Seele are just a bunch of Grateful Dead fans or something.
Reichu: Either that, or they're targeting a line of Seele merchandise at young girls. They're suckers for pretty colors. (How else to explain the commercial success of such franchises as Rainbow Brite and Lisa Frank?) But I digress. Again.
In the storyboards, not only does the logo look slightly different, it is said to belong not to Seele, but “Essene”. Considering the timing issues Wigs mentioned back in 001a, it seems odd that the name of the collective baddies hadn't been decided yet — but, then, Seele is not even mentioned until episode #14 (we are only dealing with the Instrumentality Committee before then). Interestingly, "Essene" is actually quite a bit more meaningful than “Seele”… Some quick Googling yielded the following:
The Essene brotherhood had its inception at the time of Melchizedek, the great spiritual master who lived on this planet around 1973 B. C. and was the incarnation of Jesus. … The development of the Essene brotherhood over the next two thousand years is embodied in the development of the Jewish religion. The Essenes were a Jewish sect representing an esoteric aspect of Judaism, or Jewish mysticism. The Jewish mystics studied the Kabbalah, which taught belief in reincarnation, astrology, channeling, prophecy, soul travel, psychic development, and angels, and which organized itself around the Tree of Life. (Source)
Hmm, any of that sound familiar? Also interesting is that the Essenes are often credited with the actual creation of the Dead Sea Scrolls.
It is fun to theorize which, if any, real-life occult organizations Seele is supposed to be, and this, even though it was changed in the end, provides the most “definitive” answer we are going to get. Ever since I made this finding, I've become increasingly fond of the idea that Seele represents a modern-day incarnation of the Essene: a radical Kabbalist sect mutated by the discovery of real-life "supernatural" beings and artifacts that provide tangible justification for their "faith"... and provide a means to attain the goals set forth within their "sacred texts".