David Flores is a New York photographer and filmmaker, and a member of the B&H Creative Content Team. He's put together a piece on the DSLR Filmmaker's workflow.
Though the files from Canon 5D Mk II and 7D work with most editors, he advocates transcoding to another format so "everything plays together well." He's absolutely right; I've put Canon 7D video into Final Cut Pro without transcoding, and though it mostly works, you end up having to constantly re-render things. So while you have to spend more time at the beginning if you transcode, you'll save it during the editing process.
The video below - and much of the article - centers on using Compressor to transcode to ProRes for Final Cut Pro, but he also cover's transcoding with the freeware package MPEG Streamclip (which is both Mac and PC compatible) in the article.