Is there way to find all non-ports installations in FreeBSD? I'm using 8.4 version.
I need this for audit installed binaries for system "trusted" versions.
If you need to audit an already running server then you first have to think how to get similar setup to build a trusted base for your comparison. You can install same OS version to a test machine and build a checksum DB with tools like mtree, aide etc. Then you can install 3rd party software from OS packaging system and run checksum on these new files. As you would have trusted DB with signatures, you can get same signatures on your server being audited. Then compare the results.
Creating such signatures DB should be part of post-installation steps. After base OS installation from trusted media, create a DB with signatures. If you would use a deployment system like cfengine, puppet, chef etc. you can automatize such activities. Also such tools have such auditing features built-in (comparing files' checksums).