In harsh words: There's only a barely discernible difference. In general, it doesn't matter which word you use, you equally refer to any, all, every and each object of the group (whatever the group is).
While I was sure that there's no difference at all, Toscho just posted an example where "alle" may convey a different meaning than "jeder". While "Jeder muss ein Boot bauen" is unambiguous, "Alle müssen ein Boot bauen" has two possible interpretations (The one he mentioned and the same as using "jeder").
So, there's indeed a difference. The point is that if you say "alle" you integrate all object into one group and refer to the group. The context will clarify if the group 'works' together or not.
If you say "jeder" you collect all object and refer to each object separately.
This is a similar difference as "each" and "every" in English. In most cases, the outcome is the same, disregarding your word-choice.
Finally, in my comment to your question I mentioned some possible differences in emphasis. Upon further reflection I don't go along with that anymore. If you want to stress 'each and every', you repeat the words.
Jeder, aber auch wirklich jeder...
Alle, und damit meine ich alle...
Niemand, absolut niemand...
Keiner, wirklich keiner...
Some people claim that keiner is use with a specific group while niemand is associated with a larger, unspecific 'everything'. Not sure why they claim that, but I realised that kein can be used as an adjective. For example: Kein Mensch, Kein Schwein.
If you have "Kein Mensch" in mind and you're going to replace it with an indefinite pronoun, you might tend to take keiner. Furthermore, this might be the reason that some people think that keiner is related to a specific group while niemand is less specific.
This, however, is just a guess. Rather far-fetched. There's no reason against choosing niemand instead.