SQL formatting is an area where there is a great deal of variance and disagreement... But fwiw, I like to focus on readability and think that whatever you do, consistently conforming to any rules that reduce readability is, as the old cliche goes, a "foolish consistency" ( "Foolish consistency is a hobgoblin for simple minds" )
So, instead of calling them rules, here are some guidelines.
For each Major clause in a SQL statement (Select, Insert, Delete, From, Where, Having, Group BY, Order By, ... I may be missing a few) should be EASILY identifiable. So I generally indent them at the highest level, all even with each other. Then within each clause, I indent the next logical sub structure evenly... and so on.. But I feel free to (and often do) change the pattern if in any individual case it would be more readable to do so... Complex Case statements are a good example. Because anything that requires horizontal scrolling reduces readability enormously, I often write complex (nested) Case expressions on multiple lines. When I do, I try to keep the beginning of such a statement hanging indent based on it's logical place in the SQL statement, and indent the rest of the statement lines a few characters furthur...
SQL Database code has been around for a long time, since before computers had lower case, so there is a historical preference for upper casing keywords, but I prefer readability over tradition... (and every tool I use color codes the key words now anyway)
I also would use Table aliases to reduce the amount of text the eye has to scan in order to grok the structure of the query, as long as the aliases do not create confusion. In a query with less than 3 or 4 tables, Single character aliases are fine, I often use first letter of the table if all ther tables start with a different letter... again, whatever most contributes to readability. Finally, if your database supports it, many of the keywords are optional, (like "Inner", "Outer", "As" for aliases, etc.) "Into" (from Insert Into) is optional on Sql Server - but not on Oracle) So be careful about using this if your code needs to be platform independant...
Your example, I would write as:
Select column1, column2
From table1 T1
Where column3 In (Select Top(1) column4
From table2 T2
Join table3 T3
On T2.column1 = T3.column1)
Or
Select column1, column2
From table1 T1
Where column3 In
(Select Top(1) column4
From table2 T2
Join table3 T3
On T2.column1 = T3.column1)
If there many more columns on the select clause, I would indent the second and subsequent lines... I generally do NOT adhere to any strict (one column per row) kind of rule as scrolling veritcally is almost as bad for readability as scrolling horizontally is, especially if only the first ten columns of the screen have any text in them)
Select column1, column2, Col3, Col4, column5,
column6, Column7, isNull(Column8, 'FedEx') Shipper,
Case Upper(Column9)
When 'EAST' Then 'JFK'
When 'SOUTH' Then 'ATL'
When 'WEST' Then 'LAX'
When 'NORTH' Then 'CHI' End HubPoint
From table1 T1
Where column3 In
(Select Top(1) column4
From table2 T2
Join table3 T3
On T2.column1 = T3.column1)
Format the code in whatever manner makes it the most readable...