I went to Whym a couple weeks back. It's the new place in the old Minnie's spot by Seattle Center. Got one of their scrambles. It was pretty good.
I'm not sure I'd go for dinner, but at 2:00 AM, it's one of the best things out there.
I believe they're open til 4:00 on weekdays and all night on weekends.
Honey Court in the International District is open until 3:30 on Friday & Saturday, and I believe 2 the rest of the week.
I love the Mecca (or 5 Point) for good old fashioned late night diner food. The quality is actually pretty good for a dive bar. you cant beat their grilled cheese and yummy, thick cut golden brown fries fir under $5. I also like the club sandwich and the open face turkey sandwich with mashers and gravy.
Whym is not amazing - but for late night food its not bad. The gravy and cheese covered fries are pretty damn satisfying. But I prefer the atmosphere of the Mecca.
I dunno how late you're talkin' - but Umi sake house has a great great sushi Happy Hour that starts at 11p and I think goes until 1am.