Saturn by a mile. The console, to me, represents the high water mark of their Japanese stables. I have never been a big fan of Sonic or football, so those quasi-absences didn't really bother me.
Daytona USA, Sega Rally, Virtua Fighter 2, Fighters MegaMix, Virtual On, Last Bronx, Fighting Vipers, three Panzer Games, Dragon Force, Gaurdian Heros, three Shining games (including the last great one), Sakura Taisen, two unique Sonic Team efforts, and on and on and on.
The console represented the apex of 2D gaming, and, despite the naysayers, was a damn good 3D game maker as well. Shenmue running on the Saturn looks like some of the best graphics of the 32 bit era. Sonic X-Treme, even as an incomplete and unreleased game, continues to inspire the series, (and Mario, to boot). Sega also had the 3D controller, the net-link, the twin sticks and a slew of other great gadgets.
The Saturn was also definitely a time of trial. Being a Sega fan at the time was so bizarre. It was bizarre, because Sega was quickly throwing out or never mentioning many of their greatest sellers from the MD era. No Ecco, no Eternal Champions, no Streets of Rage, no (real) Phantasy Star, no ToeJam and Earl, barely any Sonic and so on. It was completely turning the page, but it was a hell of a turn.
I think what is most upsetting about the Saturn was that it could have been so much more. Despite that, I think it represents, particularly from a Japanese software perspective, the brightest time at Sega.