Can I have my submissions separated into separate categories?

I recently created a job application form for my website where people can submit their resumes for various positions. 

Is there a way I can have the e-mails/submissions that come in separated by which job they apply for?

No actually that is no possible, however, you can download the Excel report then apply the filters.

Another solution would be to create a google spreadsheet integration and sort them out from there.

http://www.jotform.com/help/228-How-to-Integrate-Form-with-Google-Spreadsheet