I also wish The Fantasy Trip was more popular, but it's so good, there's still a fair number of people who play it. It was my first RPG twenty-six years ago, and I've been playing it off and on either tabletop or pbp all this time. I squeeze in at least a one-shot every year.
There are so many deserving RPGs that get squeezed out by D&D, it's hard to just name one. I've played over sixty systems and half of them I enjoy as much or more than D&D. I love D&D, but there are just so many genres and kinds of role-playing it does not do well even with some fairly extreme rules drift.
I wish Feng Shui, FATE, Cinematic Unisystem, to name just a few favorites had caught on better than they had (to this point anyway). There's a revolution in indie rpgs that's been going on for a few years now that is redefining what role-playing can be. We'll see how far it goes, but half my favorite games have come out in that last three years.
Also, I'm sure it varies by region, but I believe Cyberpunk 2020 was fairly popular - its success got a few other companies to put similarly themed games out on the market. I ran a Cyberpunk 2020 campaign for 3 and half years back in college and had about fifteen players over the course of it, many of whom started their own campaigns when I capped participation at eight players.
On the d20 front, I hope A Game of Thrones, Iron Heroes, and True20 all get more support/popularity. They're all brilliant.