How often do you use npm packages which are not part of atmosphere? I remember this not working great. Have things changed?
I think inevitably the meteor team will bring this into core, or something similar, and we will be able to have our mix of atmosphere and non libraries.
Iron-Router was the lead for a while.
I don't think these should necessarily be in core, but here is my list of pretty much always-installed modules:
stevezhu:lodash iron:router meteorhacks:npm meteorhacks:async aldeed:collection2 aldeed:autoform aldeed:tabular xolvio:cucumber yogiben:admin