Table aliases and simple consistency will get you a long, long way
What looks decent is breaking lines on main keywords SELECT, FROM, WHERE (etc..).
Joins can be trickier, indenting the ON part of joins brings out the important part of it to the front.
Breaking complicated logical expressions (joins and where conditions both) on the same level also helps.
Indenting logically the same level of statement (subqueries, opening brackets, etc)
Capitalize all keywords and standard functions.
Really complex SQL will not shy away from comments - although typically you find these in SQL scripts not dynamic SQL.
EDIT example:
SELECT a.name, SUM(b.tax)
FROM db_prefix_registered_users a
INNER JOIN db_prefix_transactions b
ON a.id = b.user_id
LEFT JOIN db_countries
ON b.paid_from_country_id = c.id
WHERE a.type IN (1, 2, 7) AND
b.date < (SELECT MAX(date)
FROM audit) AND
c.country = 'CH'
So, at the end to sum it up - consistency matters the most.