If you are the tube experimentation type, with the MOD100 you can mix different pairs of octal types, i.e. 6L6/EL34, KT88/EL34 etc... I've been trying some of these blends lately and have really been able to shape my tone however I like. MOD100 also allows you to bias each tube individually whereas with the MOD50 you have to buy and bias matched pairs. There is almost no difference in sound level between 50 and 100 watts and I think what matters even more is how effective the master volume is. With both amps you get one of the best MVs in the business so power level shouldn't be a deciding factor for you. The key decision points are price, weight, tube blending, number of channels and possibly feel, since I have heard that the MOD 50 is a bit saggier.
MOD100 is 75 pounds, a heavy beast, but man you gotta see the size of the transformer! You can pull 2 tubes on it if you like, but I am a basement player and I have never needed to do that because of how effective the MV is.
Don't think you could go wrong with either.
My MOD100 is going NOWHERE!