When I try to access my Windows shares from my gentoo machine, certain files are not readable, giving an error of "Permission denied", or NT_STATUS_ACCESS_DENIED when I use smbclient.

Other files on the share work fine.

The permissions set on the Windows system (for the files or [one of] the directories containing the files) do not permit you to access them. Make sure you connect as a member of the correct domain or workgroup, remembering that Windows is strange about capitalization, and verify the ACLs on the files and directories.

If you're using XP, note that files in "<system root>:\Program Files\" and ":\Documents and Settings\" are not, normally, sharable. In order to access those files, set your samba credentials file to log you on with your Windows userid and password, or as an administrator.