A quick look at using Plupload to chunk uploads to Amazon S3 and then how to rebuild the master file using Amazon S3's multi-object upload feature.
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Chunking Amazon S3 File Uploads With Plupload And ColdFusion

by Ben Nadel (on Google+)

By default, files uploaded using Plupload are uploaded in their entirety within a single form post. However, Plupload does have the ability to chunk files. When a file is chunked, it is split up into multiple parts, each of which is posted to Amazon S3 independently.

However, since Amazon S3 is not our server, we then have to initiate the rebuild of the master file from a success URL on our side. With Amazon S3, we can use the Multi Object Upload to copy-merge our chunk files into the master file.

This is meant to deal with browser limitations and to allow for some fault tolerance in the file upload; in addition to the chunking, you can tell Plupload to retry failed uploads a given number of times. This way, if there is a momentary network problem, Plupload may still successfully upload the chunk, and eventually, the entire file.