Personally, I find that code generated by
Parse::RecDescent is generally slower than a hand-coded recursive descent parser. But such comparisons really depend on the skill of the programmer.
Without seeing your language, grammar, or parser, I can't give any specific advice. In perl top-down parsers, nonterminals in your grammar generally correspond to functions and terminals to regular expressions. So eating comments should be a pretty fast operation. An excellent book on parsers and compilers is Compilers: Principles, Techniques, and Tools, by Aho, Sethi and Ullman.