TransitVis is a (very rough and no where near complete) visualisation tool for GTFS files.
It uses OpenLayers to pull in OpenStreetMap tiles and a GeoJson file with the data from the shapes file. A few short perl scripts in the util/ directory can be used to generate the geojson.
So far the easiest way I have found to work on GTFS data is to import it in to an SQLite database. I have a fork of cbick's gtfs_SQL_importer which has an additional index but will hopefully be merged back in.
At the moment it is all pretty hacky and very incomplete. A few people have expressed interest in seeing what I am up to and having it not die on a hard drive never to be worked on again. So here it is. If you line your ducks up right you will see little busses moving along the shapes from start to end at a constant speed and returning to the start to go again.
I have a few scripts in the utils directory which are handy for guessing the shape_dist_traveled field in both the gtfs_shapes table and the gtfs_stop_times tables. They aren't exactly fast nor do I claim them to be particularly acurate, but they will do the job for now.
It currently loads trips from a hardcoded date and time that lines up with my dataset using jquery's ajax library. It also dynamically loads the shape data as it needs it.
Package up the trip timings into something JSONy and use that data to set each marker's distance property.