I would use the p-value/FDR which each method returns to rank the gene list for that method in order from 'most likely to be DE' to least likely. You would then have three ranked lists of genes - you would put the actual rankings in for each gene - 1 for the top ranked, 2 for the next, etc. You could then carry out, say Spearman's rank correlation on the lists of rankings to assess agreement between the methods.
You could also decide to keep all 3 methods, and accept genes as DE if, for example, at least 2 out of 3 methods give an acceptable p-value/FDR.
From my experience, correlation should be reasonably high at the top of the list, where the methods tend to agree more on the rankings, and when the correlation gets lower, further down the list, would be where I would start to question whether the genes are really differentially expressed.