Thanks to Emily's recent blog, I've been using Start3D to create 3D "Piku-Piku" views of rover images, with mixed results.

I've been using Google Image Search on marsrovers.jpl.nasa.gov to browse left and right images to input to Start3D, but it doesn't look like I'm seeing all of the images. I'm also matching filters by filename, which isn't very efficient. How do you folks find matching left/right images?

Sometimes google can be your enemy...

Have you tried looking at the regular jpl image sites, eg for Oppy:
http://marsrovers.jpl.nasa.gov/gallery/all/opportunity.html
Pick a sol, any sol. Hazcam and navcam images are usually paired up in L/R pairs. With pancam there are fewer stereo pairs because many views are duplicated with different filters. But L2/R2 or L7/R1 usually make good pairs when they're there.