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You should look at using Batch Apex to accomplish your goals.
You cannot retrieve more than 50,000 records your SOQL calls in a single context.
However, with Batch Apex your logic will be processed in chunks of anywhere from 1 to 200 records in a batch.
You'd need to modify your business logic to take the batching into account if necessary.
http://www.salesforce.com/us/developer/docs/apexcode/Content/apex_batch_interface.htm