You can keep copyright notices and other important comments in your output using the "important comment" syntax. So for instance, if my source has this comment in it:
/*! Copyright 2010 by Contoso Corp. All rights reserved */
[note the placement of the exclamation point immediately following the "/*" sequence] the output will be:
/* Copyright 2010 by Contoso Corp. All rights reserved */
(Keeps the comment, but removes the exclamation point). This will work for both the JS and the CSS syntax.
A "leave alone" block could be a good idea. I'll have to think about how it would be implemented and what ramification it would entail. Might just treat it the same way as an eval statement.