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Most of the perl or PHP file uploads should work. I'd **definately** put the whole thing behind a login, which will eliminate many security issues. If you use perl, you can use ImageMagick to check file types and create thumbnails for display. A mysql database will store job data, and your programming should include functions for storing customer data, job specifications, updates so the customer can add more data as required, check job status, and view PDF's once you've got a proof ready. Your admin area would have any functions you need to communicate with the client.
So what have you got so far?