Joining tables in T-SQL: INNER JOINs vs. WHERE clauses

At a new employer, I'm finding a whole lot of T-SQL (1st) where tables are joined by piling them in the FROM clause, and specifying the relationships in the WHERE clause, versus (2nd) the way I was always taught to do this, by FROM one table INNER JOIN ... the rest of the tables.

Other than apparently speed, are there any issues with leaving SQL statments in the 1st manner?

My background is Access, so I'm not familiar with this, or with query optimization.

TIA
Jim

-- (1st) 11871 rows in 1 second
SELECT policy_no, sf_affinity_desc
FROM ufn_selling_agent('1-1-2008', null, null) sa, certificate c, policy p, sales_force sf, sales_force_affinity sfa
WHERE sa.cert_id = c.cert_id and
c.series_id = p.series_id and
c.cert_no = p.cert_no and
sa.sales_force_id = sf.sales_force_id and
sf.sf_affinity_cd = sfa.sf_affinity_cd

-- (2nd) Modified by me based on what I'm used to, 11871 rows in 0.? seconds
SELECT policy_no, sf_affinity_desc
INTO glfeed_selling_agents
FROM ufn_selling_agent('1-1-2008', null, null) sa
INNER JOIN certificate c ON sa.cert_id = c.cert_id
INNER JOIN policy p ON c.series_id = p.series_id and c.cert_no = p.cert_no
INNER JOIN sales_force sf ON sa.sales_force_id = sf.sales_force_id
INNER JOIN sales_force_affinity sfa ON sf.sf_affinity_cd = sfa.sf_affinity_cd