Used in the German anthem 'Lied der Deutschen' as 'Deutschland ueber/uber Alles' (germany over all others).
Used in 31337speak or netspeak meaning best, very, ultimate
Could come from the word amazing in german (Überraschen)
Gah, uber lag :(
(2) Became popular in the american language through its occurence in a phrase of the old nazi-time german anthem, re-used by punk bands ("california über alles")
(3) Is now used as a substitute for "really" or "very" etc.
(2) "...Deutschland über Alles..." (Germany above All Things)
(3) This website is über-informative