I have my business-logic in ~7000 lines of T-SQL stored procedures, and most of them has next JOIN syntax:
SELECT A.A, B.B, C.C
FROM aaa AS A, bbb AS B, ccc
The two queries are the same, except the second is ANSI-92 SQL syntax and the first is the older SQL syntax which didn't incorporate the join clause. They should produce exactly the same internal query plan, although you may like to check.
You should use the ANSI-92 syntax for several of reasons
Myself I resisted ANSI-92 for some time as there is a slight conceptual advantage to the old syntax as it's a easier to envisage the SQL as a mass Cartesian join of all tables used followed by a filtering operation - a mental technique that can be useful for grasping what a SQL query is doing. However I decided a few years ago that I needed to move with the times and after a relatively short adjustment period I now strongly prefer it - predominantly because of the first reason given above. The only place that one should depart from the ANSI-92 syntax, or rather not use the option, is with natural joins which are implicitly dangerous.