Indeed, the XML repository makes for more readable queries, plus it concentrates queries in one place. Which is why Springframework, Ibatis etc. support and encourage XML files.
One can argue whether this is the better method. I confess I still like to see my queries next to the relevant code. But I believe this is mostly a development-tool need-to-solve problem.

Shlomi

I want to add
that we used to hold our queries in the Java code, and it was horrible.
most annoying was the time it took to switch from code to shell execute. (the query formatting)
So we moved to an XML repository which is much better.
Queries are much more readable and extractable.

Thank you. Yes, I completely agree. Having a convention is the most important part; I only gave my recommendations.
Indeed I did not tackle the self join issue. Thank you for your example! (I hope I fixed your code correctly?)

I think your recommendations are fine. You are, however, missing any recommendations for how to name aliases when you use self-joins.

I find that sometimes, the alias may even be longer than the table name:

SELECT later_customer.*
FROM 
  customers AS first_customer
  JOIN customers AS later_customer ON (first_customer.cust_id = hypothetical_earlier_customer.cust_id)
WHERE 
  hypothetical_earlier_customer.cust_id IS NULL;