The only change I'm aware of is that xenon headlights, which had been optional on the 1999 540's, became standard on the 2000's. Also, I think the 2000's got optional 17" 5-parallel-spoke alloys. 17" 15-radial-spoke alloys were standard both years.
If you can, get a 2001--if you're unaware, those got the angel-eyes headlights and LED taillights with clear turn signals. Of course, if you buy a 2000, you can upgrade later--Bavarian Autosport carries that stuff.
Also, I have a 1999 BMW 5-Series brochure I got from the dealership (this was just before I bought my 1986 528e

) I REALLY LOVE the 1997-2003 5's, and the 540i 6-speeds are #1 on my most-coveted-somewhat-reasonable-car list. If you want it, I can send you my beloved brochure.