Here is an interesting conversation :

www.eggheadcafe.com/conversation.aspx

To summarize, BDC provides a better relevance to your search  results than Federated search; architectures are different, but these are 2 different ways to crawl your data.

If you have existing database or Web Services, you can import them in the BDC and display the data  in OOB web parts, Custom web parts or Custom lists.
However you web services must follow several well defined rules.

Personnaly I would go the Federated Search way, it's much easier if you want to integrate FileNet (never done it however).

An alternative to explore is CMIS...