As long as you've got foreign keys in your database I've found that Visio does a pretty good job.  I had a postgresql database with about 150 tables from four different merged projects that were connected through various foreign keys and it did an awesome job of extracting all the relationships and grouping the tables together.  The diagram had only a few overlapping lines despite extensive foreign keys.  Also, because of the foreign keys logical elements were grouped together nicely it was clear which databases most of the tables originated in.

Tool for automatically generating and laying out an entity relationship diagram?

What is the maximum number of countries meeting at a single point on earth?
Where is it?
What are the countries?

