There are quite a few games that are worth the digital asking price that aren't worth the secondhand physical asking price.

(going from US/JP PSN and US Wii/Wii U Virtual Console)

Megaman Legends 1, 2, Tron Bonne
Castlevania 3, Rondo of Blood, Chronicles, SotN
Pulseman
ToeJam & Earl
Shining Force 1, 2
Phantasy Star 4
many TG-16 games (esp. Dynastic Hero)
Namco Museum 1-5, Encore (Encore is JP only)
Harmful Park
Rakugaki Showtime
LSD: Dream Emulator (don't know much about this one, but it's probably worth the $7 or so based on how much people seem to like it)
Silhouette Mirage
Metroid Prime Trilogy
EarthBound
Kirby's Return to Dream Land
Metroid Prime Trilogy

Then there are the games I consider worth buying digitally because I think they're great:
Phoenix Wright: Ace Attorney 1-3 (either Wii or 3DS), Dual Destinies, Spirit of Justice
Picross e and 3D Round 2
Pushmo
Harmoknight

With the exception of the Ace Attorneys and Picross 3D Round 2, these are all $20 or less.