There are many ways to sort peaks out. For instance, there is a script for RRDtool that removes obviously irrelevant spikes [1].
The vast majority of hundreds of thousands metrics are common for any node/server actually, so predefined recipes/settings should be used for them. Only aplication-level metrics for only in-house applications have to be tuned manually.
[1] http://oss.oetiker.ch/rrdtool/pub/contrib/removespikes-20080...