I not only use formatting to help organize things, I also include comments for every subquery. I also make sure that every column returned by every query and subquery have proper table aliases and that the aliases actually mean something especially when self-joins are present.

Depending on the performance of the code, I may also break the code up into smaller and tighter pieces and store the interim results in a TempTable or two so I don't have to work with such large data sets. Sometimes, the performmance improvement is quite dramatic. I recently took such an "all-in-one" query (35 tables joined including some self joins) that virtually crippled the server it was running on for 45 minutes and divided it up in such a manner. The code now runs so fast that it usually doesn't even show up on the Task Manager performance chart.

Getting back on topic, the splitting up of the code also allows for more pertinent comments for each section of the code.