I have been putting togethor an expression that needs to do something similar.
the finished product is: 
/(?:((["'])(?:(?:\\\\)|\\\2|(?!\\\2)\\|(?!\2).|[\n\r])*\2)|(\/\*(?:(?!\*\/).|[\n\r])*\*\/)|(\/\/[^\n\r]*(?:[\n\r]+|$))|((?:=|:)\s*(?:\/(?:(?:(?!\\*\/).)|\\\\|\\\/|[^\\]\[(?:\\\\|\\\]|[^]])+\])+\/))|((?:\/(?:(?:(?!\\*\/).)|\\\\|\\\/|[^\\]\[(?:\\\\|\\\]|[^]])+\])+\/)[gimy]?\.(?:exec|test|match|search|replace|split)\()|(\.(?:exec|test|match|search|replace|split)\((?:\/(?:(?:(?!\\*\/).)|\\\\|\\\/|[^\\]\[(?:\\\\|\\\]|[^]])+\])+\/))|(<!--(?:(?!-->).)*-->))/g
Scary right?
To break it down, the first part matches anything within single or double quotation marks
This is necessary to avoid matching quoted strings
((["'])(?:(?:\\\\)|\\\2|(?!\\\2)\\|(?!\2).|[\n\r])*\2)
the second part matches multiline comments delimited by /* */
(\/\*(?:(?!\*\/).|[\n\r])*\*\/)
The third part matches single line comments starting anywhere in the line
(\/\/[^\n\r]*(?:[\n\r]+|$))
The fourth through sixth parts matchs anything within a regex literal
This relies on a preceding equals sign or the literal being before or after a regex call
((?:=|:)\s*(?:\/(?:(?:(?!\\*\/).)|\\\\|\\\/|[^\\]\[(?:\\\\|\\\]|[^]])+\])+\/))
((?:\/(?:(?:(?!\\*\/).)|\\\\|\\\/|[^\\]\[(?:\\\\|\\\]|[^]])+\])+\/)[gimy]?\.(?:exec|test|match|search|replace|split)\()
(\.(?:exec|test|match|search|replace|split)\((?:\/(?:(?:(?!\\*\/).)|\\\\|\\\/|[^\\]\[(?:\\\\|\\\]|[^]])+\])+\/))
and the seventh which I originally forgot removes the html comments
(<!--(?:(?!-->).)*-->)
I had an issue with my dev environment issuing errors for a regex that broke a line, so I used the following solution
var ADW_GLOBALS = new Object
ADW_GLOBALS = {
  quotations : /((["'])(?:(?:\\\\)|\\\2|(?!\\\2)\\|(?!\2).|[\n\r])*\2)/,
  multiline_comment : /(\/\*(?:(?!\*\/).|[\n\r])*\*\/)/,
  single_line_comment : /(\/\/[^\n\r]*[\n\r]+)/,
  regex_literal : /(?:\/(?:(?:(?!\\*\/).)|\\\\|\\\/|[^\\]\[(?:\\\\|\\\]|[^]])+\])+\/)/,
  html_comments : /(<!--(?:(?!-->).)*-->)/,
  regex_of_doom : ''
}
ADW_GLOBALS.regex_of_doom = new RegExp(
  '(?:' + ADW_GLOBALS.quotations.source + '|' + 
  ADW_GLOBALS.multiline_comment.source + '|' + 
  ADW_GLOBALS.single_line_comment.source + '|' + 
  '((?:=|:)\\s*' + ADW_GLOBALS.regex_literal.source + ')|(' + 
  ADW_GLOBALS.regex_literal.source + '[gimy]?\\.(?:exec|test|match|search|replace|split)\\(' + ')|(' + 
  '\\.(?:exec|test|match|search|replace|split)\\(' + ADW_GLOBALS.regex_literal.source + ')|' +
  ADW_GLOBALS.html_comments.source + ')' , 'g'
);
changed_text = code_to_test.replace(ADW_GLOBALS.regex_of_doom, function(match, $1, $2, $3, $4, $5, $6, $7, $8, offset, original){
  if (typeof $1 != 'undefined') return $1;
  if (typeof $5 != 'undefined') return $5;
  if (typeof $6 != 'undefined') return $6;
  if (typeof $7 != 'undefined') return $7;
  return '';
}
This returns anything captured by the quoted string text and anything found in a regex literal intact but returns an empty string for all the comment captures.
I know this is excessive and rather difficult to maintain but it does appear to work for me so far.