I make a periodic practice of searching our node_modules folder for files that shouldn't be there and reporting bugs against the offending projects.
Usually that's been pretty effective, and now the total cruft is around a megabyte whereas before it was somewhere north of 50MB all told. (Conditions apply).
coverage reports, test results, build detritus, etc.
The one I'm still debating, because it's becoming a serious problem for a couple of our libraries: should the tests be included in .npmignore or kept along with the library? I'm not sure what the right answer is there. Test sizes especially including fixtures can creep up quite a lot over time. I know what I'd like it to be, but I'm not sure I can win that argument with a bunch of maintainers on different projects.