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If you want to be sure that your pages get found, then link to them with straight html. If you want to see anchor text influence helping the target page show up on relevant search results, then you need straight html links. If you want PageRank (or any search engine's measure of link popularity) to affect target pages, you need a straight html link.
[edited by: tedster at 8:16 pm (utc) on April 23, 2006]
If you're in a situation where you're absolutely stuck with javascript menus on a site, you might consider adding straight html links within a <noscript> tag, but that is liable to look pretty ugly to visitors who do have javascript turned off. (The noscript appearance will depend on how many links there are in the menu and where the menu is on the page).