Longest running in years, I've been playing the original Legend of Zelda since 1988. It's not a very long game, so no idea on total hours I've put in over the years.
Other games I've played multiple times and have repeatedly gone back to for uncounted hours over the years:
Star Trek: Birth of the Federation
Europa Universalis: Rome
Making History: The Calm & the Storm
Back before my friends and I all got married, we used to get together once a week and play sports games. As many as 6 of us would get together and play seasons of football controlling different teams, or creating wrestlers and playing out careers. So during that time I've also logged a ton of time into:
Tecmo Super Bowl - NES (mainly 1990 - 1998 until Franchise mode became a staple of the Madden series)
Raw 2 - Xbox (played heavily 2003 - 2006)
Smackdown vs Raw 2007 - Xbox 360 (General Manager mode made this our staple wrestling game from 2006 on)
Madden 13 (Wii U) <--- I've gotten over 4 years out of this game since EA decided never to release a football game on Nintendo since. My best friend still does come over to play this one.