Cpanel generates a 600MB backup file for one of my websites which is a bit too big to download regularly. What I am thinking is to get another account with a different host and FTP the backup file there.
DreamHost is very useful for taking backup.
It comes with SSH and REAL crontab.
You can use rsnyc, wget -m, whatever.
Very easy and pretty cheap ($22.40 or less for the first year, with the promo ocde).
I recently bought NetFirms account for $10 /year, too.
(I haven't checked the TOS if I can use it for backing up, though).
Depending TOS, it can be an alternative.
Even if their MySQL or webserver is slow during daytime, it can be good enough for keeping/taking backup.