Best way to backup and transfer everything?

I'm using Time Machine to back up my Macbook Pro. I'm going to reformat the Macbook Pro, and I may continue using it or I may want to put all of the files from it onto my current iMac. Either way, I do not want to copy over any of the applications or system files from the Macbook Pro, just the data files. What is the best way to do this?
1. Should I even bother with Time Machine OR should I just take the time to go through every folder on the Mac looking for files to copy over?
2. Are data files ever saved to application folders?
3. Is there anything in Library or other locations besides documents, downloads, music and movies I should check?
Thanks.

Hi Tom,
Thanks for the help - good questions - if not too much trouble I'd like to know several ways
- for now let's say it is a Project and that I would also like to ...
1 - keep all media (maybe for a future re-edit possibility)
or
2 - Just keep the media used in the project

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