<p>Which SQL statement is faster?</p>

<pre><code>SELECT TOP 2 c1.Price, c2.Price, ..... c49.Price, c50.Price
FROM Table1 AS c1, Table2 AS c2, ..... Table49 AS c49, Table50 AS c50
WHERE c1.Date = c2.Date AND c2.Date = c3.Date ..... c49.Date = c50.Date
ORDER BY c1.ID DESC

        OR

SELECT TOP 2 c1.Price, c2.Price, ..... c49.Price, c50.Price
FROM (Table1 AS c1 
 INNER JOIN (Table2 AS c2 
    ........
  INNER JOIN (Table49 AS c49
   INNER JOIN Table50 AS c50
  ON c49.Date = c50.Date)
    ........
 ON c2.FullDate__ = c3.FullDate__)
ON c1.FullDate__ = c2.FullDate__)
ORDER BY c1.ID DESC";   
</code></pre>

<p>Basically I need to extract 2 rows from each table to produce a summary periodically.
Which statement is faster?</p>

WHERE would usually be better but the best way is
case by case
and throw this into profiler, or simpler yet
display execution plan
.  Folk often have very strong opinions on which approach is fastest/best in theory but there is no replacement for actually tuning according to the data you actually deal with as theories applicable change depending on your data load.
If you do not have
real data
in your app yet, try and create some realistic stress data.  This will continue to be useful for testing.  Then schedule time to tune once the application is live.