For inner joins I have not really noticed a difference (but as with all performance tuning, you need to check against your database under your conditions).
However where you put the condition makes a huge difference if you are using left or right joins. For instance consider these two queries:
SELECT *
FROM dbo.Customers AS CUS
LEFT JOIN dbo.Orders AS ORD
ON CUS.CustomerID = ORD.CustomerID
WHERE ORD.OrderDate >'20090515'
SELECT *
FROM dbo.Customers AS CUS
LEFT JOIN dbo.Orders AS ORD
ON CUS.CustomerID = ORD.CustomerID
AND ORD.OrderDate >'20090515'
The first will give you only those records that have an order dated later than May 15, 2009 thus converting the left join to an inner join.
The second will give those records plus any customers with no orders. The results set is very different depending on where you put the condition. (Select * is for example purposes only, of course you should not use this in production code.)
The exception to this is when you want to see only the records in one table but not the other. Then you use the where clause for the condition not the join.
SELECT *
FROM dbo.Customers AS CUS
LEFT JOIN dbo.Orders AS ORD
ON CUS.CustomerID = ORD.CustomerID
WHERE ORD.OrderID is null