So I did a whole bunch of searching and found some excellent information about a leaky sunroof. Check the drain holes and make sure they're not plugged, check the drip tray and make sure it hasn't come loose, check the 'gutters', check the rubber seal, etc.

So I did ALL those things on my 4Runner and everything was okay, but it was still leaking.

However I did notice that the front metal (where the rubber seal bumps up against when you close it) had quite a bit of dirt/dust on it. I thought "hmm, I wonder if that dirt is causing it not to seal properly?" So I took out a damp cloth and wiped the metal clean, as well as the front of the rubber seal just for good measure. Closed it up. It's been raining pretty much solid here in Calgary since the weekend when I made the change, and it's bone dry. No more leaks.

I didn't notice "try cleaning the dirt off" as one of the solutions, so I thought I'd share.

 

Yes, don't forget the obvious!