Assuming you mean the Toccata and Fugue in D-minor (the most popular one), my favorite LP is Marie-Claire Alain on Erato.
If you can find it, another Direct-to-Disk recording, with spectacular sonics, is "The Power and the Glory, Volume I," with Lloyd Holzgraf on the organ of the First Congregational Church of Los Angeles (M&K Realtime RT-114, from 1978).
I can't comment on the performance, though, because I only played the recording once, about 25 years ago. Played at a modest level, the deep bass that was present set the windows in the room into severe vibration, and caused paint chips to fall from the ceiling. :-)
No other recording has ever done that in my experience, not even the Telarc 1812 Overture.
My Telarc 1812 CD version has a warning on the cover. The accompaining literature furthers "WARNING! The cannons of the Telarc Digital 1812 are recorded at a very high level. Lower levels are recommended for initial playback un-til a safe level can be determined for your equipment".
My version of The Power and the Glory warns, "Osha approved personal protective hard hats are recommended upon first review of this material until a safe listening environment can be determined"!
See if you can find on vinyl "The Golden Age of the Organ"
E.Power Biggs takes an organ tour of Germany and Holland playing organs that were extant when Bach was alive. The tuning is a little different from today's standard and it allows you to hear it as Bach might have. It includes much more than just the Toccata& Fugue in D minor, good hunting
03-30-11: RcprinceSome excerpts from the jacket:
Some of the reasons for the remarkable sound are: 11,848 pipes under the guiding hands of a great master; three simultaneous organs with 198 feet separating the two giant organs played antiphonally and blended; a neo-classical stone cathedral of enormous size with superb acoustics, real 32-foot ranks.... In addition to having so accurately captured the fundamental frequencies of the 32 foot ranks, we have also accurately captured the natural beat frequencies generated by these huge pipes with an energy content which lies well below 16Hz.Isochronism -- LOL!