SQL JOIN Syntax in MS SQL
Queries of the second type fall under what some call a SQL antipattern (check out the nice book written by Bill Karwin). The second query almost resembles a Cartesian JOIN whose WHERE clause has to be evaluated on the fly.

The first is cleaner and the order of execution can be better managed.

You could compare both ways by


getting the EXPLAIN plan for each and seeing if execution time is the same
creating a third type that refactors the query and get its EXPLAIN plan and running time
see if all indexes are being evaulated the same for the three query styles


You are better off going for the JOIN syntax because you can generate result sets with LEFT JOINs and RIGHT JOINs that may be far different from (maybe more desirable than) INNER JOINs.