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After upgrading to Firefox 3.0.1, inline youtube links stopped working.
I tracked it down to "AdBlock" plug in.
Disabling that makes youtube work again, but now ads are back.
It's probably an ad-blocking list you subscribed to that got a little overzealous. I made my own block list and Youtube still works, but Google ads are still blocked.
You should be able to see what rule is blocking youtube by clicking the red ABP icon and looking over things...