As the owner of a 6-speed 540, I hate to say it, but my preference for the 6-cylinder E39 is with an automatic, at least with a 2000 or newer model year (so you get the 5-speed auto). My rationale:
1) Auto smoothness complements the 6-cylinder engine's buttery smoothness
2) My impression from test-driving a 2000 528 5-speed was that manual shifting was a lot of work for not much reward, due to (a) the 6-cylinder's lesser torque requiring a lot of shifting to keep the engine in its sweet spot in rpms, and (b) the relatively long throws of the E39 shifter (a complaint of mine with my 540 as well). My arm and leg were getting tired on just an hour-long test drive!
3) For resale, especially with the 6-cylinder models, I think the market would favor an automatic over a manual.
In the end, it's your personal preference. So I'll say what I tell everyone who asks this question (and it's asked often): test drive as many examples of both types of cars as you can find and then make up your own mind, keeping in mind your projected driving routes/mileage/habits/traffic/etc.
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2006 Honda Odyssey EXL-RES
2006 Honda Accord V6 EX-L Sedan
1999 BMW 540i 6-Speed (Sold to M3UOND on 9/21/06)
1991 Honda Civic Si - Occasional Beater
Last edited by Eric S.; 08-23-2006 at 08:41 PM.