I got this off motionbased, saved it as a text file to remind myself of the differences

There is a limit to how many waypoints can be used to make up the route/course in both TCX and GPX. I do not know the exact numbers but from what I remember TCX can handle longer course.

-------------------

Course
- file extension is TCX
- file gets placed in Courses folder on Edge
- Can be created on the Edge or in Training Center based on past ride, many online programs can be used to create them from scratch
- Cannot recalculate on the Edge
- Allows for virtual partner use
- No turn by turn warnings unless you add them in manually using Training Center or online Course creator

Route
- file extension is GPX
- file gets placed in the GPX folder
- Two types of Routes can be created, one that supports autorouting and one that is a track

Autorouting version
- Recalculation can be set to Automatic, Prompted or Off
- No virtual partner
- Turn by turn promps occur automatically
- Can be created using one of many online tools or Mapsource if you own the DVD version of maps
- Can only display one route onthe map at a time

Track version
- No Recalculation
- No virtual partner
- Not sure about turn by turn directions but I am pretty sure it does not support them
- Can be created using Mapsource if you own the DVD version of maps, not sure if the online sites support it or not
- Can display mutiple routes of this type on the map at a time

This is by no means a complete list but will definitly aid in your confusion.