Man d_h speaks truth. Additionally, the Moog was used as a white-noise source for 'I Want You (She's So Heavy)' (heard near the end), but this was purely for noise effect and not musical melody.

And I always thought that the repeating sound in 'Baba O'Riley' was done by putting the organ's Banjo setting through the VCS-3's sequencer, which wouldn't be that hard to do. (Watch Rog in the Pompeii film, and also remember that the drums in 'On the Run' were fed into the VCS-3).