Smile.co.uk get this right
I bank with smile.co.uk, who get this right - they never send a link in the e-mail, always telling you to go to the home page and log in.
It's really not rocket science, but I suspect marketing departments of insisting on it looking pretty and being trackable, and to hell with the security...
Smile also have a "secure messages" system, so you get an e-mail like the following when they need your attention. No scope for phishing here!
12th July 2010,
Hello Mr Collins
We've sent you a secure message. Please log on to read it.
Thanks
smile