My personal favorite is the new This Is Spinal Tap commentary track. They got all four of the principal actors back together, and they did a seemingly ad lib and totally hilarious discussion over the entire movie, including them shutting up to see some of their best musical numbers. See the movie, see the commentary track, see the movie again. (I also hope to hear GeoffRomer's choice of best commentary track) -BenjAzose
UHF has a great commentary track, because it's just Weird Al joking around the entire time. Also, the Star Wars prequels have interesting commentary tracks since you learn a lot of fun facts from the special effects and sound guys.--AlexBobbs
The dvd for Dr. Horrible's Sing-Along Blog contains Commentary! The Musical!. Though it isn't so much commentary, as just additional songs Whedon wrote, on subjects ranging from Asians being type-cast in Hollywood to an iPhone game the cast got addicted to (and occasionally, also about the actual filming of the show). Definitely my vote for most creative commentary track. Instead of the movie's soundtrack, you get... a second soundtrack, for free! --AdamField