After the name of the table in the FROM clause you can specify the alias, eg:
Code:
FROM ACME.dbo.Documents AS Doc1
INNER JOIN ACME2.dbo.documents AS Doc2
(you may not need the keyword AS, but I think it helps with clarity)
Then you use the alias in the rest of the query, instead of the table name, so it becomes:
Code:
SELECT Doc1.filename, Doc1.LatestRevisionNo, Doc1.WorkingVersionModified,
Doc2.filename, Doc2.LatestRevisionNo, Doc2.WorkingVersionModified
FROM ACME.dbo.Documents AS Doc1
INNER JOIN ACME2.dbo.documents AS Doc2
ON Doc1.filename = Doc2.filename