Accessify.com – why you should use the acronym tag to increase accessibility. The page also explains the difference between an acronym and an abbreviation:
So, to decide whether you should use an <acronym> or <abbr> tag, use the test above – “Can I say the abbreviation as a word in its own right?”. If yes, use an <acronym>.
Personally, I find the difference pretty pointless in mark-up. Couldn’t (X)HTML have just had an <annotation> tag </annotation> for footnotes, tooltips, etc?