The first big difference between the Entity Framework and LINQ to SQL is that the EF has a full provider model which means that as providers come online (and there are several in beta now and many which have committed to release within 3 months of the EF RTM), you will be able to use the EF against not only SQL Server and SQL CE but also Oracle, DB2, Informix, MySQL, Postgres, etc.
Next there is the fact that LINQ to SQL provides very limited mapping capabilities. For the most part L2S classes must be one-to-one with the database (with the exception of one form of inheritance where there is a single table for all of the entity types in a hierarchy and a discriminator column which indicates which type a particular row represents). In the case of the EF, there is a client-side view engine which can transform queries and updates made to the conceptual model into equivalent operations against the database. The mapping system will produce those views for a variety of transformations.