Although they are somewhat similar, I don't see this thread as movies that grossed more on DVD than they did in the box office, or even movies that didn't bank at the box office. I see it as movies that have created a large [cult] following -- especially once they hit DVD/VHS -- regardless of the money they've made.
My list would include, but is not limited to:
Army of Darkness
Being John Malkovich
Big Lebowski, The
Big Trouble in Little China
Boondock Saints
Breakfast Club, The
Clerks / Mallrats / Chasing Amy / Dogma / Jay and Silent Bob Stike Back
Crow, The
Dawn of the Dead
Donnie Darko
Fight Club
Goonies
Grease
Half Baked
Labrynth, The
Lock, Stock, and Two Smoking Barrels
Monty Python and the Holy Grail
Napoleon Dynamite
Night of the Living Dead
Nightmare Before Christmas, The
Lord of the Rings
Lost Boys, The
Office Space
Princess Bride, The
Requiem for a Dream / Pi
Reservoir Dogs
Rocky Horror Picture Show
Rushmore
Saturday Night Fever
Scarface
Shaun of the Dead (in the UK)
Snatch
Spinal Tap
Star Wars
Trainspotting
Of course, most of these movies had cult followings long before they were released on DVD or VHS. I'll leave it to you to pick which ones were reborn once they hit DVD.