Often an offline system file repair with the MS DART corresponding to whatever version of Windows will identify a patched file. In truly nasty situations, however, it's also possible to run a script or short program to check the hashes manually, provided internet access is available. There are databases available (such as
this one) which can be used to check hashes relatively quickly via DNS queries. Plus, many hashes are common between systems and can be manually whitelisted for quick verification without any need for DNS querying. Finally, when in doubt, it's always possible to check Company information and verify the file with an online service such as jotti or VirusTotal.
I find that this method is quite effective when combined with the usual manual disinfection via powerful tools such as OTL. I use these tools within a PE by loading the remote registry hives and performing analysis on the registry offline. It's a lot of setup work, but once you get used to it, almost nothing can hide.