Unfortunately, none of the client complaints have been in writing. My next goal is to try to get one in writing to pass along. Since posting this, I've talked with a couple of the other associates who have the same issue and they're going to try to get something in writing as well. If we go to the partners with enough, maybe one of them will lay down the law.
I also like the idea of simply rejecting any e-mail that is in all caps.
I have flat out told her not to do it. Unfortunately, the inusbordination issue here is huge and I'm more or less stuck with it. The partners somehow think that she's irreplaceable and the only associates she seems to have a problem with are the females.
The passive aggressive evil me wants to start sending all of my messages to her in all caps. 
NRB80's Rule No. 1 of being an associate - responsibility without authority. It sucks. I had some issues trying to get my secretary to work *for* me. And do things my way. Because, ultimately, it's my license to practice, not hers. Of course, the partner has worked with her for 20 years so woe be it to any associate that gives her a negative review...
As to a comment later in the thread about secretary's sending emails - many clients do not like to see billing timekeepers (attorneys, paralegals, etc) forwarding documents, filings, etc. because they assume it ends up on the bills. My secretary is empowered to send emails with filings, documents from the other side, etc. along with a message to clients. However, I am lucky enough that my secretary does this well.