The documentary on the 12 Monkey's CE.

I second the mention of the Ghostbusters commentary. It is one of the few commentaries with true re-watchability.

I also want to add the video commentaries on both Mallrats and Dogma, as well as the sports-style commentary on the Swingers SE.

Other then the above, I also enjoy the "tour of the set" soundstage tours (often hosted by a cast member) on the CSI season sets (Miami and Vegas).

The deleted scenes on Spinal Tap, particularly the Bruno Kirby getting high sequence.

The Hamster Factor on 12 Monkeys

The uncleaned-up start of the movie on the original Elite release of "Night of The Living Dead"

I thought the easter egg on The Ring was pretty good where you could watch the entire video.

Similarly thinking, the option to play the entire dream sequence on Final Fantasy: The Spirits Within, and maybe perhaps the easter egg on the same disc with the movie characters dancing to Michael Jackson's Thriller.

Removing of Laugh Track from MASH & Sledge Hammer.

Wow, that's weird . . . I just watched FF again this morning. I'll never understand the malignment against that movie.

Favorite:

Fast Times at Ridgemont High: Cameron Crowe/Amy Heckerling Commentary & map of key locations

Other Faves:

Repo Man LE Tin: The bonus CD soundtrack & the California license plate replica cover

Freaks & Geeks LE: 2 bonus dvds + the yearbook

Scarface Boxset: Bonus DVD of original 1932 version and the money clip

Universal Classic Monster Coffin Set: The coffin box

Halloween Extended DVD: The LE film cell

The 2 hour making of Phantom Menance Documentary on Star Wars Episode I: The Phantom Menace

Also, the 3 hour documentary on the Indiana Jones Box Set was fantastic.

The 2 1/2 hour making of "Alien" documentary on the Alien Quadrilogy Set

I personally love watching docs as long as the material isn't fluff like on a EPK

Early Fave: The follow the white rabbit special feature on The Matrix was what made DVDs cool when showing it off back in the day.
Another nod to Roger Ebert commentaries
Another nod to the hidden version of T2 on the Ultimate DVD

I do agree with a lot that has already been posted, but I will chime in with:

Any Conan O'Brien Commentary on the Simpsons sets. Truly excellent!

The Cannibal! The Musical drunken commentary was a riot also.

"Chicks who love Guns" on Jackie Brown

the "farting" soundtrack on WET HOT AMERICAN SUMMER

Good call!

The documentary about the lost cartoons from the Looney Tunes set was pretty cool. Now if we could get those cartoons restored and uncut on DVD (especially the ones made for World War II).

I also enjoy the sound-effects only tracks on the Toy Story UTB, it's cool to just listen to those sounds and nothing else, especially in 5.1.

"Best bonus feature ever" advertised, if i may take a different angle, would be english subtitles...!

Tarantino commentary and the Trivia Track on Pulp Fiction were the best I seen so far.

any dvd that has trailers in anamorphic WS AND 5.1 sound!
(i still can't believe the trailers on matrix reloaded/revolutions were not 5.1)

another nod to the music video on 'ghost world' - totally bizarre AND catchy

the hilarious short films on 'tenacious D - the complete masterworks'

how could anyone forgrt the nude sceen index an Eurotrip unrated

I love documentary "The Beginning" on the Star Wars Episode I DVD. I've probably seen it about seven times.

I nearly busted a gut laughing at this

but we do skip the beach scene right???

the deleted segment from Heavy Metal and alternate Rough Cut of film