I have been trying to figure out this special effect in the song "Amy Hit The Atmosphere" by the band Counting Crows... it´s the rippling sound, just in the beginning of the song... sounds like it´s some kind of guitar with a pedal effect? Or perhaps an Organ?

Here is a link to the song on youtube http://www.youtube.com/watch?v=feom_uT7tTk]YouTube - Counting Crows - Amy Hit the Atmosphere.wmv - It´s the first sound you hear...

It says they use B-3 Organ and Sitar in this song... but I find that sitars wont sound anything close to that... unless with some kind of effect?

Any help is greatly appreciated.
Sounds like a vibrato pedal to me.

You do mean the clean guitar in the left and right channels, correct?
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That is a SICK effect! It sounds like a lot is going on there...wah, whammy, who knows...my guess is the sustain is coming from an ebow and he's using a delay of some kind that can also be manipulated with a foot swtich.
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rotary speaker, delay, auto wah, I think.
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I can't really guess what instrument it is, (honestly, it could be anything) but I'm skeptical that it would be just a single effect going on. I've heard synthesizers, chorus/vibrato, flangers and echoes that all contain parts of that sound. I do FOR SURE hear a wah in the background somewhere.

I will say this: Try and see what some research of your own might yield.

I'd start here: http://www.youtube.com/watch?v=-ouX_r5lfBk&feature=related

I found the EHX effectology video series to be really interesting, and inspiring.