Many have accused Muslims of being "silent" in the face of terrorism. Though examples abound in the blogsphere, where it is practically conventional wisdom that Muslims consent by virtue of their supposed silence (examples: Steven, James, Brian). This stereotype also penetrates deeply into traditional media, with William F Buckley's essay "Are we owed an apology?" being a prominent example.
From Muhabajah.com, is this comprehensive list of links and resources on Islamic perspectives against terrorism (hirabah), essays by prominent Islamic intellectuals and clerics condemning terrorism, statements by muslim leaders, and even a section on muslim military personnel.
In addition to these, there is also this statement condemning 9-11 by the leaders of the American Muslim Alliance, the American Muslim Council, the Council on American-Islamic Relations, the Muslim Public Affairs Council, the Muslim American Society, the Islamic Society of North America, the Islamic Circle of North America, the Muslim Alliance in North America, and American Muslims for Jerusalem. Almost all of the country's 7 million muslims are represented by these groups.
And, the Grand Mufti of Saudi Arabia condemned the 9-11 attacks as well.
In general, though, islamic condemnnation of terrorism is dull news here in America's media. Here in Houston, the various Islamic groups had "open Mosque" days and other community-peace programmes after 9-11, which drew mild interest at best. Later, a firebrand gave a anti-Semtic speech at a local campus and it made headlines. One firebrand x 10,000 media points = a score of 10,000. 100 peaceful muslims x 1 media point = a score of 100. AltMuslim has a nice roundup of other community outreach efforts by Muslims during Ramadan, but again, this is not a winnable PR battle (another reason I don't think it's worth the effort, counter to SDB's opinion).
 Muslims do NOT owe anyone an apology for 9-11.