Has a beneficial mutation ever been documented?
The answer depends on what you mean by "observed".

Bacteria acquire antibiotic resistance genes all the time, for example. This happens 'in the wild', but you can see in the lab that bacteria can become resistant overnight - I'd call that 'observed'.



There are many papers about the emergence of antibiotic resistance (not that I'm suggesting this is the only observable beneficial mutation).

In this paper, for example, several spontaneous mutations are induced in H. pylori in the lab in a short space of time:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC90364/

In this paper, estimation of mutation rates are attempted in the emergence of resistance:
http://aac.asm.org/content/44/7/1771.full

It should be pointed out however that the timeframes can vary wildly. If a bacteria acquires a resistance gene by horizontal transfer, for example, this could be considered virtually instantaneous. Spontaneous mutations may take longer to emerge, and might only do so in the presence of steadily increased selection pressure, by contrast.