I have a 2 year WHP visa to Canada ( I'm Australian) which I got in May last year, I had to come home in July last year for family reasons, problems with my bank (still angry about that one) etc.. the list goes on

Anyway I want to go back in July this year until my visa expires in May 2012, Do I need to return to Australia and apply for another one or can I got to the US and re-enter that way?

I know I can't extend the visa and I have to reapply.

If your work permit remains valid, then you should be able to simply travel back to Canada (directly or through the USA). There is nothing here that suggests that you would otherwise be prohibited from doing so.