Normally, when an application starts, it has to first find the location of all of the libraries it needs. This can take time, and will cause the application to load slower. Updating the prebindings will record all of the links between applications and libraries. This will speed application launch, but will probably not speed up your system very much (except for application launch).
Its probably not worth running update_prebinding on a regular basis. this only needs to be done once, until more applications are installed. This system is 'prebound' to begin with (though it wasn't with earlier versions of OSX -- which is why this command started circulating). Also, I believe when the Installer app says its optimizing things at the end of an install, it is actually running update_prebinding. So its probably not worth the worry of manually updating things.