The opening of this anime is full of references. I've caught all of them except this one. What is the meaning of this and in which language is it written?
It's an image of what is referred to in the show as the Dead Sea Scrolls, or specifically the Secret Dead Sea Scrolls, which are the blueprint that SEELE use to implement the Human Instrumentality Project.
That said, the inscription looks suspiciously more like impressionistically-drawn kanji than any of the Aramaic or Hebrew I can find on Google. For example, the first two characters bear a pretty close resemblance to 天使, or "angel".
Dead Sea Scrolls were real things, and they were written mostly in Hebrew, and some in Aramaic. However, the shown text doesn't have any similarities to both of them. Although some of the characters look like Japanese characters (e.g. 天,丸,乙,せ,き), they were not written in Japanese either (it doesn't have any meaning).
Researching this further, it seems it's written in some kind of Angelic Script. Some of the real-world examples are Celestial (previous link), Malachim (angels, or messengers), and Transitus Fluvii (or Passage Du Fleuve). Note the similarities: the shape, and dots at the end of the strokes.
Image courtesy of CirqueDeTruth on AboveTopSecret forum
Considering the similarity, and also the script's reference to Angel (this series has many references to Angel, nonetheless), it seems to be written in Angelic Script. However, there are no same characters with any of these, so it might be just another Angelic Script created specifically for this series, (or Japanese characters written in Angelic Script, who knows). Hence, the meaning is also not yet known.
Reference: Japanese Yahoo! Answers for mentioning 天使文字【てんしもじ】 (tenshi moji, or Angelic Script)