Mostly I used a self written panel/dock and for some time also wf-shell (the reference/default shell). But imho there are are lot more options because Wayfire implements a lot of Wayland protocols.
For applications like file manager I just used what I thought fit the best like e.g. mostly from the mate and xfce environment.

You mean why I switched away? Has actually nothing todo with Wayfire itself. I had it installed on a very customised Debian Sid installation and started to have less time to tinker with my system and wanted/needed something more stable and polished.