Hi!
I like the following track much and want to have a similar organ sound in my track, maybe someone of you know how it was created?

Organ sound from 3:08

Sounds like a manually performed arpeggio using an a preset in a modeling synth. This is not a manipulated sample of a real organ. You can tell by the slight glide modulation from note to note, which is not a sonic feature a real organ is capable of producing. 

Start by browsing through presets in synthesizer VI's.