See in the demo Page URLs report. Since 0.6.2, entries are linked to the actual page URL. If you click on faq/plugins/ for example, you see that the page "index" links to http://piwik.org/faq/general/#faq_52
Instead, URLs should link to the canonical URL without the hash part. The hash must be removed at Tracker time.
Note: the tracker must still receive the hash, for future uses (eg. detect campaign parameters in the hash), but the php code must discard it.
I guess for some pages it would even make sense to display those hash parts in the Page Urls report. Most Ajax-driven websites aren't changing the url often. In most cases only the hash part changes for history. Facebook might be a good example for that. Maybe it might be the best solution to make that behaviour configurable.
by default, we would record the hash tag, users could disable it.
Cool, later we will want to have the setAllowAnchor, because some campaign parameters are sometimes set in the hash tag, but we can do it later (also requires change in piwik.php to discard the hash tag bit in all cases after campaign parameters were parsed)