Each year the EPA rules got tougher. 2006 was also the last year a Stage One download actually did any good as far as enrichening the air/fuel mix (according to my dealer tech).
If you get ahold of a parts books, you can see the different mufflers listed by year. The 2006 has the cat in the touring mufflers, the 1995- 2005 and the 2007 does not. Part number 80463-06, entitled, Catalyst Equipped Fits '06 Touring Models. Screaming Eagles were not offered for 2006 except with a cat, but came back in 2007-2008 cat free when the EFI module was changed and the ox sensors added . In 2007 they were 50 state legal, but in 2008 the same mufflers are only 49 state legal.
In 2009 (California) and 2010 (all fifty states) rules got increasing strict, hence the cats are back.
Page numbers 540-542 in the 2008 parts book.
Other models (Dyna, softtails, sportys, etc) have their own mess of different mufflers as well.
Think that's confusing? You should see the different cam grinds each year to keep the EPA happy. The 2006's I believe, were the first cams without an overlap on the timing. Adding the Andrews 21's really livened up our motor, and I'd recommend them to anyone with an '06.