I have been porting oracle selects, and I have been running across a lot of queries like so:
SELECT e.last_name,
d.department_name
FROM employees e,
Google "Oracle join syntax". the (+) is used for different flavours of outer joins. I think the first one you showed is a Left Outer Join, and the second one is a Right Outer Join. I haven't seen this notation for quite a while, so I could be a little off, but hopefully, this gives you enough info to hit Google and get the right answer.
UPDATE:
So you wants a tool to do it for you? I have heard that SwisSQL can do something like this, but if most of the queries are simple enough you can probably write a little script that does it for you. OMG Ponies answer nicely shows the pattern for converting from old to new syntax.