'is not within a known GOPATH/src' error on dep init

Go makes this choice so that there is nothing like a CLASSPATH (ie: Java) to deal with. You specify a $GOPATH that has a consistent src tree inside of it. If your repo makes references to particular git commits (rather than the ones checked out into $GOPATH/src/github.com/$githubUser/$githubProjectName), then those will be in the ./vendor directory of your project.

If you have a different Go project that uses a completely different set of checkouts, due to versioning issues, then you can have multiple $GOPATH values to deal with that.

How can I use dep without moving Go projects to %GOPATH%/src?

Not at all.

Go projects require that your project is within its path.. So first do a $ go env to find out where that is. Lets say it says /home/turgut/go move the project that you downloaded that needs the dep to: /home/turgut/go/src/myproject then cd /home/turgut/go/src/myproject and try the dep ensure command now.