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For SSH, mostly just a bash command prompt if I know what I am transferring and whereto/-from, or rsync if archiving or syncing large quantities of files. Otherwise I just type the URL (ftp:// or ssh://) into Nautilus' address bar (Unity and Gnome Shell's default file browser); it usually just works.

Sometimes I fall back to gFTP if the FTP server is finicky.

I prefer WinSCP for FTP and SSH on windows I prefer Cygwin OpenSSH, but putty is just fine.
scp for single files (bash autocompletion works on remote paths for me), sftp for a browse and rsync for large numbers of files.

I don't really use regular old ftp, but if I need to then I usually just install the command-line ftp client, and uninstall it when I'm done.