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I agree with DavidCo. The biggest threat to the security of online banking seems to me to be social engineering scams - ie tricking you into revelaing your logon details on a fake site.
Trusteer Rapport should go a long way toward stopping this (provided you set it up to protect the real site in the first place of course)!
The other main threat I suspect is from keyloggers. Rapport says it prevents these on its protected sites too.
Keyscrambler is another free option for this I suppose.