There are some excellent companies out there that can provide a broad range of site audits for you. Moz has compiled and excellent list here: http://a-moz.groupbuyseo.org/community/recommended
Because they weren't on the list and I have a tremendous amount of respect for the knowledge and experience this company has under one roof I'd also mention Rimm-Kaufman (RKG)
Prices can vary wildly, ranging from free audits to audits that are $10,000 or more, so it's important to consider where your company is and what's needed and take it from there. Here's a great post on site audits from the RKG blog:
Building a Better SEO Site Audit
Hope that's helpful info. Also, if you've got someone savvy on your team, and you have more time than you have money, here's great site audit template (given as part of Annie Cushing's presentation at Search Love Boston in 2012) that can really go pretty deep and help you construct one on your own:
http://www.seerinteractive.com/blog/craziest-internet-marketing-audit-checklist-on-the-interwebz
It includes links to an already formatted GoogleDoc that templates everything you need. Brilliant.