Of my -brief- experience with both, MRTG is meant for creating pretty graphs of metrics and Nagios is meant for monitoring up/down of systems and services. Since you said your trying to monitor performace, then MRTG (and whatever scripts you in turn write) shold give you plenty of info on trends, etc in the performance category. If you want to get paged/emailed when X happens, you probably want nagios. Both are a little involved setting up, but they are really two different applications.