Your question is rather broad ranged and it’s hard to just give "best practice" audit policies without knowing a lot more.
For instance if you are looking for security practices it depends on what your organization needs to protect and what it needs to prevent. What sort of government regulations must you adhere to? Like I am in the banking industry and we have tons of regulations that we have to follow that do not apply to a lot of other industries. We have to audit at least two times a year and have at least one government audit. They audit things like our OU policies, password policies, lockout policies, software policies, patch policies, user access policies, backup policies, firewall policies, Internet access policies, email policies, screensaver’s, logout policies, documentation and a ton of other things.
If you are talking about a general audit just to know what sort of hardware and software your users have on desktops etc you can use a software that will audit pretty much all of that for you and keep it in a nice DB for future reference. Once software that we run is called Track-It by intuit.
If you are talking about just a base security scanner that will audit your network for vulnerabilities you can use the free baseline security scanner from Microsoft (which works very well) or do like we did and purchase something like Retina security scanner by eEye Digital or languard by GFI LANguard. (We bought a scanner just because of the reporting features)
Two sites I recommend taking a look at are
and
Cert has a ton of information about security practices.