Networking helps here. I've never gotten a job where my resume had to be filtered through HR first. You need to know someone who is or knows a hiring manager. Get out there and make friends!

echoing what mlitchard said. Networking is a big help. Besides that, look at what is on the job posting. Try to use the same key words in your resume/cover letter. Not sure how well it would work, but addressing differences in the cover letter could work to get it past the HR and into the manger's hands.