I definitely always do my JOINS (of whatever type) in my FROM clause.
The way I indent them is this:
SELECT fields
FROM table1 t1
INNER JOIN table2 t2 ON t1.id = t2.t1_id
INNER JOIN table3 t3 ON t1.id = t3.t1_id
AND
t2.id = t3.t2_id
In fact, I'll generally go a step farther and move as much of my constraining logic from the WHERE clause to the FROM clause, because this (at least in MS SQL) front-loads the constraint, meaning that it reduces the size of the recordset sooner in the query construction (I've seen documentation that contradicts this, but my execution plans are invariably more efficient when I do it this way).
For example, if I wanted to only select things in the above query where t3.id = 3, you could but that in the WHERE clause, or you could do it this way:
SELECT fields
FROM table1 t1
INNER JOIN table2 t2 ON t1.id = t2.t1_id
INNER JOIN table3 t3 ON t1.id = t3.t1_id
AND
t2.id = t3.t2_id
AND
t3.id = 3
I personally find queries laid out in this way to be very readable and maintainable, but this is certainly a matter of personal preference, so YMMV.
Regardless, I hope this helps.