Like most musicians, I have a special fondness for Bach. But there are pieces of Bach that are my particular favorites for various reasons: and they are usually specific reasons. I wonder if other musicians have their particular favorites. These are mine:
The motet Komm, Jesu, komm (BWV 229) because I got to sing it with an adult chorus when I was a teenager.
The D minor Fugue of the second book of the WTC. I remember when when I was a kid we got the Henle edition of the WTC. My older brother declared that the E-minor Fugue was his fugue because it had the longest subject, or something like that. I was forbidden to play it, so I promptly picked the D minor Fugue as mine and I have retained ownership.
The D minor Toccata, BWV 913 because it is so completely limitless and so modern. I didn't hear it until I was an adult, working at a radio station. It was Trevor Pinnock's recording that hooked me.
Cantata 78 because it was my first cantata. I had a volume of tenor arias with instrumental obbligato parts, and the first one in the book was for tenor and flute from Cantata 78. I bought a recording and fell madly in love with the whole piece. My father told me that Cantata 78 was the first cantata he played when he used to play church jobs in Cleveland. I thought that was extremely cool.
The B-flat Partita because of Dinu Lipati's recording of it.
The St. Matthew Passion, for reasons that I simply can't articulate.
The A minor and D minor Violin Concertos, which, when I was a flutist, were forbidden flute-fruit (I always wanted to play them on the flute, but they never sounded right). Now I can play them on the violin whenever I want to hear them.
The Cello Suites and the Violin Sonatas and Partitas. The happiest memories I have from my childhood are the mornings when I would lie in bed and hear my father practice the Bach Cello Suites on the viola. He would also practice the Violin Sonatas and Partitas on the viola, so it took me a long time to figure out what was what.