Have you ever altered a SharePoint Database?

Well, if your answer is affirmative I recommend you this article: http://support.microsoft.com/kb/841057/en-us

Audit data in SharePoint and its impact in DB size

If you are using the SharePoint audit features you need to know which impact have in the size of your DB. A bad audit configuration may cause that the content and SSP database grow permanently.

In the case of a site collection with the audit enabled (http://office.microsoft.com/en-us/sharepointserver/HA100997261033.aspx) you will see the space used by auditing in the table AuditData in the content database. On the other hand, if you are using a BDC application definition and you have defined an entity make sure that in your entity definition sets the audit property properly (http://forums.msdn.microsoft.com/en-US/sharepointbdc/thread/ea208a3b-fd3b-4508-882e-466371c1a53c/).

But if you have enabled auditing for several months is possible that you need to free up space in your disk. In this case the only supported way is through API (very slow solution). For that reason I recommend that review the requirements of your SharePoint solutions and only enable the Sharepoint audit options that are required.

Update: In the Infrastructure Update there is a new stsadm command that allows to trim the logs: stsadm -o trimauditlog –enddate 20080704 –databasename WSSContent123456 (Thanks kezoe)