"best" version for "Toccata and Fugue D minor?

Don't overlook Michael Murray on Telarc.

While the Murray recording is good, I still am lukewarm about his performances, though there's never a technical mistake. I prefer Christopher Herrick on the Hyperion label, probably influenced in part by the fact I've gotten to know him and am impressed both by his scholarly approach to Bach as well as his playing. The Guillou is also a good version, has a lot more fire than Murray's. And if you want something completely different and don't mind some liberties taken in registration and a very dry organ sound, Virgil Fox's recording, both the direct to disc vinyl and the CD version, is an exciting, though admittedly eccentric, version.

I realize that you asked about redbook CD recordings, but for the benefit of others, I'll mention two LP's and one SACD that feature good versions of the "D-Minor".

I'm partial to these versions of the "Toccata and Fugue in D Minor":
1. "Magnum Opus", an LP released by Wilson Audio in the 1980's and featuring the Flentrop organ in St. Mark's Cathedral in Seattle (n longer in print, but well worth owning if you find a good used copy);
2. a direct-to-disk LP by CrystalClear featuring Virgil Fox playing the organ in the "Crystal Cathedral" (Garden Grove Community Church in Los Angeles. (This was re-released on an inferior CD version on the budget LaserLight label. For more info, click on this link: http://www.amazon.com/exec/obidos/tg/detail/-/B000001VNE/103-7419193-2295801?v=glance)
3. Sony Classical SACD re-issue of E. Power Biggs playing the 4 antiphonal organs in the Cathedral of Freiburg. This SACD has great sound and very good performances of Bach's great Toccatas and Fugues, including the "D-Minor". On a good surround system, the sound is IMPRESSIVE.

SD, the Fox recording is the one I was speaking of, and was released, I believe on the Bainbridge label, as The Digital Fox. Sound was never that great, even on the vinyl, as the organ seems quite close-miked and accordingly dry, but you're right, the digital version is not nearly as good as the vinyl.

I know you asked for CD but there is an LP version that really should be heard. E> Power Biggs has been mentioned, one particular album set he put out has him doing an organ tour of Germany and Holland, playing on organs built by APR SCHNITGER(1648-1719) organs Bach himself might have played on. The sound is quite different from modern organs, lighter, airier, higher, if you can get a hold of it and have it transferred to CD you will be quite amazed. I know I was. It is on Columbia Stereo M2S 697 or Mono M2L 297.
Sorry for the digression but it should be heard to hear what Bach wrote/composed as he would have heard it.