> ...but I still feel that prototype-based languages have a certain 
> conceptual elegance that is lacking in class-based alternatives.

It's interesting the part western philosophy played in language design, I 
tend to agree with you about the conceptual nature of class vs prototype 
inheritance, but class based inheritance is easier for me to use, easier to 
lay out in my mind.

Here's an interesting read on the subject:
http://www.helsinki.fi/~jppesone/papers/kandi.html

Summary:
From an ontological point of view the prototype-based languages win. There 
is little evidence of a strange platonic realm of categories, but 
class-based languages don't necessarily have to be realist in their 
ontology - a language can include universals and "Santa Claus" without 
committing to realism (von Wrigth 1972, 198). Unless the prototype-based 
languages include some notion of categories they lack something 
psychologically very important: the capacity of categorization.

-Jeff