What Sonya said was more along the lines of evaluate (as used in accuracy, reliability and validity) but the idea of 'why' was spot on.
From Wikipedia:
Justify: To demonstrate or prove to be just, right, or valid.
So you are basically providing evidence as to why you chose to carry out an experiment in a particular way. What made the experiment a good, fair or well-grounded one? It's similar to validity (in the discussion section) except you are demonstrating the worthiness of the method used (no criticisms and problems need to be addressed).
Some general examples I've used before for Chemistry include:
> The test was safe and was easily carried out.
> The test used a wide variety of substances to accommodate for the different _________.
> The experiment produced highly observable results (easily experienced through the senses e.g. clearly seen, loud/distinguishable sounds, strong smell/taste/touch sensations).