...In this category, can a true "best" ever emerge? Having said that, I can honestly tell you that this set is magnificent, having owned and enjoyed it since 1997. My only quibbles are that (1) some of Alain's registrations, while at the very least "good," are upstaged in several places by other performers whom I have on recording, and that (2) the recorded sound gives plenty of room to the organs' tones - sometimes _too much_ room, a problem that is also present on Alain's _Art of Fugue_ set, with the result that contrapuntal clarity gets smothered in a sea of reverb in some places (mind you, the "cloud of sound" approach works well with Bach's music, but I prefer clarity). Alain's technique and tempi, on the other hand, are untouchable. The disc with the trio sonatas is particularly good!
I actually consider having multiple performances of Bach's music a must - my favorite set is Lionel Rogg's on Harmonia Mundi, but he is, by no means, definitive - and neither is Alain. They complement each other quite nicely!