Excel is a popular choice because there have not been many alternatives if any - you need to have a look at Analytixds.com. A purpose built solution for mapping at an enterprise level, that allows you to generate SSIS packages from the mappings... a ton of other features that are miles ahead of excel, and robust metadata features as well (impact analysis, lineage, truncation alerts driven off the mappings). Have a look. Excel is only the answer if you don't know about this tool - there is a wealth of information on the site, and you can get an evaluation license for free.
Sam Benedict, VP Strategic Accounts
Analytix Data Services - Mapping, Code-gen Platform for SSIS/All ETL Brands