End of "Great" BART was July 2005
Last year, there used to be trains plasti-wrapped with "Best Transit System in America". We haven't seen them this year (duh!).
I peg the big change to AUG05, just after the BART union got their new contract.
Before: train announcements were for next two trains, and trains were ALWAYS on time (set your watch by 'em!).
After: announcements ONLY for the next train (often wrong), and the trains were NEVER on schedule (it was more of a "plan" or a "guide").
In BART's defense, the morning trains starting being reliable ~JAN06, and the afternoon trains have ALMOST been reliable since APR06.
Of course, now we have the "Trans-Bay tube delay-of-the-week" (things are OK, or REAL bad).
My guess: The JUL05 union pact has some early-out incentives that convinced a WAY-KEY mid-level operations manager to bail, and they are just now getting a competant replacement.

Ridership peaks in
Ridership peaks in September. More riders mean it takes longer to load and unload trains, which mean more delays. 20 seconds per station, adds up. Hot weather makes trains unreliable, just like automobiles.
I agree they have really
I agree they have really been going down hill the last year. I predict in the next year or two something horrible is going to happen (like a derailment)and then it will come out how horribly they are being run. There will probably be legislated more accountability for the managers
Oh, and one more BAD decline
Oh, and one more BAD decline in service:
Pre-AUG05, the SF to Pittsburgh line was ALWAYS 9 or 10 car trains.
After: It was even *6* car trains in the afternoons, and most commonly 8 car trains. A couple months ago, BART put out fliers that they had studied usage patterns and concluded longer trains were appropriate on SF--Pittsb.
I wish *I* could get a couple $K for such a profound conclusion.
(I took a 3PM train today: 8 cars, and 10min late)