Some thoughts/comments:

• does a rss feed fit your need? (http://www.nytimes.com/services/xml/rss/) You can just loop over the links adding the 'print-friendly' part to the query string, and save them all locally -- saves you some of the traversing ... (or does your palm have a rss reader?)
• WWW::Mechanize recommends Spidering Hacks from O'Reilly
• be sure to take full advantage of the abilities of the find_all_links() method of WWW::Mechanize
• There appears to be a scraper framework here: WWW::Scraper (and described here: WWW::ScraperPOD)

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