Space Mountain is very popular. Seems to do exceptionally well in polls, not to mention its perennially long lines. Splash Mountain also draws insanely long lines when it's warm enough outside, and Indiana Jones is a popular one too. Soarin' is one of DCA's most popular rides, seemingly along with ToT, TSMM, and Screamin'.
Indiana Jones is the most popular ride in DL imo. It's ALWAYS busy. There are times when Splash aren't very long (night, early mornings). The other candidate obviously is Space. I think the vast appeal of Indy overcomes Space Mountain's theme-less coaster. All amazing rides, but I give Indy the edge. Best ALL AROUND ride in the world imo. Big sentence I know.
You have to take into account that Finding Nemo Subs and TSMWM (to name just two), are both pretty recent rides so they're drawing in some of the heavier crowds. However, Indy, Space, and Splash, and a few other older ones aren't that recent and have continued to keep up those long lines. Peter Pan and Alice lines are also pretty much always long.
"Well I don't know about you folks, but it's way past my bedtime."