I think this is a difficult question to answer - I do not really see why the majority of usability evaluation methods would not work in this context e.g. Think aloud, observational techniques, there are heuristic sets specific to e-learning - it might be worth asking if people have used methods that did not work -
Most of my current research is on (adult and University) e-learning and blended learning. Experiments are not possible or un-ethical. students are (in my case) from many countries in both Europe and Asia. The paradigm that seems to work is action research.
1. try to identify issues that point to needed improvement or point to new opportunities
2. find potential solutions (look at design patterns from analogous design domains)
3. apply
4. assess what happens, what learners think, what teachers experience;
5. back to 1.
4 requires careful selection of tricks and tools to get relevant feed back of the stakeholders. If you want i would be happy to tell my secrets, which will only work in certain contexts.
I think you may want to search in the human-computer-interaction literature. Many studies I've read, rely on the TAM (technology acceptance model), which becomes quite handy for these kind of research questions. Currently I write a paper with a former student of mine who wrote about the usability of web based trainings.
If you're interested in user experience why not ask the user? I did a study for my MSc thesis on student experience of elearning. I used a qualitative design methodology and it was v.interesting to find that a common theme that emerged was the difficulty students faced with written communication . As far as practicalities, you could employ interview methods using Skype, etc so that you can include students from different countries (of course time differences can prove problematic). I think when you have a clear idea what aspects of usability (and from which perspective) you would like to explore this will help you decide what evaluation method to use.