I'd do it manually as well. Not worth the chance that things will go wrong when using third-party tools that can't really know how other software's installers and data works (and where those details may change over time).
I tend to keep all the installers for things I use, so if I need to reinstall the OS I can just go through that folder installing the things I still use, or installing things at the point I actually need them, depending on if I know I need it or just think I might. Combine that with a password manager that supports attachments, or similar tool for storing registration details etc., and it doesn't take long at all to build a new machine. Most of the time is taken updating Windows itself, which is still an inexplicably slow process.