The nice part of the second method is that it helps separates the join condition (on ...) from the filter condition (where ...). This can help make the intent of the query more readable.
The join condition will typically be more descriptive of the structure of the database and the relation between the tables. e.g., the salary table is related to the employee table by the EmployeeID column, and queries involving those two tables will probably always join on that column.
The filter condition is more descriptive of the specific task being performed by the query. If the query is FindRichPeople, the where clause might be "where salaries.Salary > 1000000"... thats describing the task at hand, not the database structure.
Note that the SQL compiler doesn't see it that way... if it decides that it will be faster to cross join and then filter the results, it will cross join and filter the results. It doesn't care what is in the ON clause and whats in the WHERE clause. But, that typically wont happen if the on clause matches a foreign key or joins to a primary key or indexed column. As far as operating correctly, they are identical; as far as writing readable, maintainable code, the second way is probably a little better.
