IDACompare is a plugin for IDA which is designed to help you line up functions across two separate disassemblies. IDACompare also contains a signature scanner, where you can save known functions and then scan new disassemblies against them looking for key functions. It has tools for sequentially renaming matched functions, as well as porting user specified names across disassemblies. This plugin has been designed with Malcode analysis in mind. It should work equally well for patch analysis. See readme.chm for more details.