Most SQL dialects accept both the following queries:
SELECT a.foo, b.foo
FROM a, b
WHERE a.x = b.x
SELECT a.foo, b.foo
FROM a
LEFT JOIN b ON a.x = b.x
The first way is the older standard. The second method was introduced in SQL-92, http://en.wikipedia.org/wiki/SQL. The complete standard can be viewed at http://www.contrib.andrew.cmu.edu/~shadow/sql/sql1992.txt .
It took many years before database companies adopted the SQL-92 standard.
So the reason why the second method is preferred, it is the SQL standard according the ANSI and ISO standards committee.