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The webkit team published a terrific article about the terrible effect that multiple external javascript files can have on browser performance. Drupal6 has a terrific feature called javascript aggregation which I encourage folks to enable on your production sites. It is found on the admin/settings/performance page. While you are there, enable css aggregation as well.

If you use an external ad network, I can almost guarantee that they are using just the sort of bad behavior that this article describes. If you suspect that your ads are slowing down your web pages, try browsing with javascript disabled. If it suddenly gets fast, your ad provider is a problem. Unfortunately, ad networks have been using external includes and document.write for years despite performance concerns. I get the impression that chaning their architecture is hard or undesireable so they choose to slow down the pages of their clients.