@Jeromero: Welcome to Webmasterworld (some of us forget our manners) (Smiling!).
What we use is based on what we need to track. A few websites... smaller. A lot of websites... larger. A multi-million biz requires something entirely different as the scale is enormous. It also makes a difference as to what you are tracking. If one is interested in the number of websites, passwords, domain renewals, etc, then Excel is a fine product. If one is tracking referrals, keywords, etc., then a more robust database will be necessary. If reporting on these aspects then either custom queries in the database or commercially available packages might be required.
In all cases just about everything starts with the raw access logs.