In preparing the work of the new Ph.D. student that will arrive this fall, I think a reading of there two posts "The myths of bioinformatics software" by Dr. Lior Pachter (GS) and the response by Dr. Titus Brown (GS) can help a lot. While I do not marry the negativist attitude of Patcher, I cannot deny that many of his statements are, in my experience, correct. I endorse more Brown's position, however.
I suggest that Ph.D. applicants look carefully both the positions (and the intricate series of links). For me, I certainly remain with GPL. At the same time, I would warn the applicants that I am oscillating towards a thesis topic which would sound like "Design Patterns for Hydrology" (not forgetting, certainly what I wrote on GEOtop 3.0).
P.S. -I also totally endorse this Brown's statement: "From my few involvements with working on non-free software, I would also add that selling software is a tough business, and not one that automatically leads to any profits; there's a long tail, just as with everything else, and I long ago decided that my time is worth more to me than the expected income from selling software would be. (I would be thrilled if a student wanted to try to make money off of our work, but my academic work would remain open source.)". I saw so many colleagues that believe they can sell their software or keep it close, failing miserably and missing the leadership they could have. I know also some remarkable exceptions though (Hydrus, Flo2D especially).