I prefer putting the comma at the beginning of the line (this makes dynamic sql much easier). I prefer putting and/or at the beginning of the line. I indent multiple items like case statements in the select. I use parens for join statements with multiple join conditions. I separate the select/from/where clauses with a blank line when a section has more than one line.
select
t1.col1
, t2.col2
, t3.col3
, (case when t1.col1 = 'Y'
, t3.col2from table1 t1
join table2 t2 on t1.col2 = t2.col1
join table3 t3 on (t1.col3 = t3.col1
)where t1.col1 > 0
and t2.col2 <> t1.col4
order by
col2
, col1
limit 100