So you're talking games originally released as digital-only that later got a physical release I assume, correct?
Best of PSN Volume 1 (When Vikings Attack!, Sound Shapes, Tokyo Jungle & Fat Princess)
Journey Collector's Edition (Flow, Flower & Journey)
Minecraft (available for pretty much everything)
Plants Vs. Zombies (also available for pretty much everything
)
PopCap Arcade Vol 1 (360 - Bejeweled 2, Astro Pop, Feeding Frenzy, Zuma)
PopCap Arcade Vol 2 (360 - Peggle, Feeding Frenzy 2 & Heavy Weapon)
Worms Collection (PS3 & 360 - Worms, Worms: Ultimate Mayhem & Worms 2: Armageddon)
Worms Revolution Collection (PS3 - Worms 2: Armageddon + 4 DLC packs & Worms: Revolution + 3 DLC packs)
...there are more, I'll look them up later if no one beats me to them. Gotta run for now!