My criteria for masterpiece status:
1. Use every constraint of the given art form and genre to enhance the work without an obvious way to improve on the original design.
The hardest to qualify for, and sort of unfair to several genres. RPGs (which try to emulate a believable world under ridiculous assumptions and limited budget/time) tend to fail that one on principle. The "improve on the original design" bit means the game should NOT be able to survive a genre switch.
2. Be enjoyable.
This includes not being morally repulsive, as well as having navigable interface, palatable graphics, reasonable difficulty, etc.
3. Leave an impression and/or have replay value.
This includes just thinking about the game because it's awesome, trying new strategies, seeing other plot branches/reactions to dialogue options, replaying a game with a plot twist to see all the hints you missed, and waiting for it to be released IT'S BEEN 12 YEARS GODDAMN.
In no particular order:
- Immortal Defense (name your price, min $1.75) - tower defense
- Spider and Web (free) - text adventure
Runners-up:
- Planescape: Torment ($9.99) - RPG
As close to a masterpiece as an RPG could get, neatly bypassing several design obstacles. However, blatant trap options in a game that tries very hard to remove the need for saving and loading are unforgivable.
- Escape from St. Mary's (free)
Would have been just as awesome as a graphical adventure, thus fails the "can't survive a genre switch" criterion.
- Portal, 2007 version (probably unpurchasable)
Since steam is mandatory, achievements have to count as an inseparable part of the game to be considered for masterpiece status.