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I remember reading somewhere that SQL Azure is going to terminate long-running queries. Is there a time limit on how long a query can run against a database before it is terminated? Where I work, I run complex queries against large tables that take about 5 minutes each.
Azure will terminate web-requests that are IDLE for more than 1 minute and that are made over the load-balancer (meaning from the outside to its web servers).
Azure will also throttle your slow-running queries, but only if they take resources away from the other tenants in the SQL server instance that your database is in. I do not believe there are any published statistics as to precise metrics when such throttling will occur.