For me it's Chrono Trigger. I always want to play it. I want to show it to my children. I hope it will be regarded as a masterpiece for generations to come.
I take timeless to mean that it is still just as good today as the day it was released and that the game's quality isn't related to the time period in which it was released or the hardware it was released on. Dates and hardware are included in case you want to go play them. (You should if you haven't)
Soul Calibur (1999 , Dreamcast)
Project Gotham Racing (2001, Xbox)
Top Gear (1992, SNES)
Tempest 2000 (1994, Jaguar)
Rock N Roll Racing (1993, SNES)
Transport Tycoon Deluxe (1994, PC)
Tetris (1989, Gameboy or perhaps the NES version)
Silent Hill 2 (2001-ish, PS2 or Xbox)
The Elder Scrolls III: Morrowind (2002, Xbox or PC)
I absolutely love Morrowind, but I'm torn whether to call it timeless. It's got a clunky interface, but that interface is also so much a part of the feeling that grips you when you play it.
The graphics are definitely not doing it favors at this point.
It was definitely fun to get into for a bit though. I literally started playing Morrowind for the first time about 3-6 weeks ago.