Both are EXHELLENT ftp clients. If you're not interested in FXP (server to server) transfers, then Filezilla should be your choice (use the latest 2.18b release) which does everything but not FXP. Easier to use than SmartFTP, and stable enough for me.
Now if/when SmartFTP will add the option to save the session ques for transferring them later (this is currently available only for the global ques) it will be the best FTP client I've ever met- and I have used dozens. Not that it is bad as-it-is now, quite the opposite, but I'd like to see this feature implemented.
Currently using Filezilla for normal transfers, and Total Commander 5.51 for FXP jobs.