As a webmaster I've been custom to using cPanel for as long as I can remember and I love using it. So, what's your favorite file manager? What do you use to upload and edit files on your site?
I use the NppFTP extension for Notepad++ to edit files (html, php and css), and generally use Filezilla as an FTP client to upload anything else (images generally). I tend not to use the file managers built in to panels like cPanel. If you meant what's my favourite control panel, I guess I'd go with cPanel, but that's because I'm most used to it.
FlashFXP has been my favorite for years, I piked up the full version like 5 years ago and haven't looked back.
Pretty much the same though I've gotten to like cPanel file manager quite a bit lately for working on client's sites when there is no shell access. You can zip/unzip files server side which saves quite a bit of time.
I use a combination of filezilla and notepad ++. I also use the cpanel legacy file manager to quickly edit files if I'm already logged into cpanel.