I've been asked about "more than two questions" several times and I still don't quite get what this is supposed to mean.
Of course you can compare as many conditions as you like with DESeq  you just have to do so pairwise.
If you have two conditions A and B, you may ask: Is the expression of my favorite gene larger in A or in B? How would you phrase such a "larger than" question with more than two conditions?
In the context of linear models, it is also common to ask: Given several treatments, does any of them have a significant effect, i.e., you test against the null hypothesis: None of the treatments have an effect. (Then, you may get a significant result, if you have evidence against the null even though the signal is not strong enough to tell you which condition is the one out.) This can be done with DESeq, too, with the GLM functionality, but I haven't seen many actual use cases yet where this contrast made sense.
