Thanks for contributing, everyone! That so many of you decided to go above and beyond my request in the OP by including runners-up has inspired me to do a follow-up list of my own second choices! So here they are...
JC's Runners-Up List
1987: The Great Giana Sisters
1988: Hidden Agenda
1989: Golden Axe
1990: Balloon Kid
1991: ToeJam & Earl
1992: Dragon Warrior IV*
1993: Day of the Tentacle
1994: Final Fantasy VI**
1995: Solar Eclipse
1996: Tomb Raider
1997: Tomb Raider II
1998: Nancy Drew: Secrets Can Kill
1999: Urban Chaos
2000: Perfect Dark
2001: Luigi's Mansion
2002: Nancy Drew: Ghost Dogs of Moon Lake
2003: Primal
2004: Baten Kaitos: Eternal Wings and the Lost Ocean
2005: Harvest Moon: Another Wonderful Life
2006: Rule of Rose
2007: Peace Maker
2008: Shin Megami Tensei: Persona 4
2009: Muramasa: The Demon Blade
2010: Final Fantasy XIII
2011: Sword & Sworcery EP
2012: Thomas Was Alone
2013: The Stanley Parable
2014: Never Alone
2015: Ori and the Blind Forest
2016: Ittle Dew 2
2017: Night in the Woods
2018 (so far): Iconoclasts
*This game is known as Dragon Quest IV in its native Japan.
**In a break with my pattern, I chose this title instead of the American one from the time for the sake of clarity.
Bonus: JC's Favorite Multi-Year Releases
1. Kentucky Route Zero
2. The Legend of Heroes: Trails in the Sky
