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Remove:
.eqn equations??
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You can generate equation files on demand just when you need them instead of during every compilation.
At "Tools --> Options --> General --> Processing", turn off "Automatically generate equation files during compilation".
For those rare times when you need equation files, run "Start Equation Writer (Post-synthesis)" and/or "Start Equation Writer (Post-fitting)" at "Processing --> Start".
When I use equation files, I turn on "Automatically generate HTML-Format Report Files (.htm) after design processing" at "Tools --> Options --> General --> Processing". This results in HTML equation files with hyperlinks that make it easy to trace backward through the equations.
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Unknown:
...
.qip MegaWiz something...
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Starting with QII 8.0, use the .qip files. When you add the .qip file to the project, you don't have to manually add the other individual MegaWizard files to the project.
After running a MegaWizard that produces a .qip file, you will get a prompt to add the .qip to the project unless you have turned on "Automatically add Quartus II IP Files to all projects" at "Tools --> Options --> General".
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Unknown:
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.cmp Component declarations
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This is a VHDL component declaration file optionally generated by the MegaWizard. The option is on the MegaWizard Summary page. This file is the component declaration for insertion into your source file that instantiates the component. The _inst.vhd file that you can select on the same MegaWizard page is a template for the instantiation of that component.
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Unknown:
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.dpf No idea what this is
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Inside this file it says "pin_planner". I haven't looked up what this file does. I don't know whether there is ever any value in keeping it (it might be useful if you do more with the Pin Planner later in the same design), but I doubt that this file is ever necessary to reproduce your results when you recompile.