replaced by or replaced with

Strangely, dictionaries don't seem to be a lot of help here. According to Oxford Advanced Learner's Dictionary it looks as though they're interchangeable -
'replace somebody/something with/by somebody/something -
"It is not a good idea to miss meals and replace them with snacks." '

But Longman's has this example - "They replaced the permanent staff with part-timers".- where I don't think "by" would work.

And in this example from the Free Dictionary - "the manual worker is being replaced by the machine" - I'm not sure "with" would really work.

And here are two from Merriam-Webster's:
"I replaced the old rug with a new one."
"Paper bags have been largely replaced by plastic bags."

In fact all the active examples with a preposition I can find in dictionaries have "with", and all the passive ones have "by". So It looks to me as if "with" goes better with active clauses and "by" with passive clauses.

Ngram certainly suggests that in the passive "replaced by" is much more common than "replaced with" - http://books.google.com/ngrams/graph?content=replaced+with%2Creplaced+by&year_start=1800&year_end=2000&corpus=15&smoothing=3&share=

And it seems to me to do the opposite in the active, but I'm not 100% sure about how to do a wild card here. - http://books.google.com/ngrams/graph?content=replace%3D%3Ewith%2Creplace%3D%3Eby&year_start=1800&year_end=2000&corpus=15&smoothing=3&share=

There is a suggestion on another forum that in the passive version, if the thing doing the replacing is the agent, it should be "by", but in the plastic bags example, the bags are hardly the agent, so I don't really go along with that.

And the commenter then gives this example - "Employees were replaced with robots" - which seems to work, but compare it with the Free Dictionary's very similar - "the manual worker is being replaced by the machine"

The Free Dictionary example and the second M-W examples are about general situations, and the "employees" example is about a specific occasion, so perhaps that might also have something to do with it.

Re: "...so It looks to me as if "with" goes better with active clauses and "by" with passive clauses...", I'm not sure that really tells the whole story, but it certainly seems on the right track. I'd like to propose the following (completely without justification):

"Paper bags have been largely replaced by plastic bags."

means that paper bags are no longer used. Plastic bags are now in common use, serving the same purpose, making paper bags obsolete.

"Paper bags have been largely replaced with plastic bags."

means that paper bags were, say, physically on the shelves in some actual storeroom, and someone removed most of them, putting plastic ones in their place.

Just a thought.