TakeruK, your numbers are different from what I got using the supplied calculator listed above.
For 25k, taxes would be $2331 or 9.3% for current tax and using proposed tax the 40k would be 3,336 or 8.3%. I placed zeros in all other sections of the calculator. This is about a 30% increase but it only $1005 or $83.75 per month which is still a lot under the $650 claimed earlier in this thread.
By the way, 49k for tuition is very high. I had looked at a variety of places and the numbers are all over the place for tuition. Cornell's tuition varies between $20-30k while in state at the University of Kansas is only $7341. This makes me agree that the value of the education is not fully reflected on the tuition because, while Cornell might have a better program is it really 4 times better?
Regardless of how much extra students will have to pay because of this the universities will need to do something. They have to place a value on it or else they would let people in for free but if there is a value then it has to be taxed when they waive it for grad students. So they need to increase the stipend to cover the taxes for tuition or come up with some other way of covering it. Of course, how much are the taxes going to be can very depending on personal situations (single, size of stipend, other income, etc.)