In some cases, 50+ may offer no help, or offer diminished returns, but for the most part skills over 50 increase damage/ability like at any other level.
Styles: Your style damage is based solely off of your spec in the style you are performing. Dragonfang has a larger style bonus with 50+11 than...err, well you can't have it below 50, but pretend it was at 39+11.
Hamstring hits harder with 50+11 CS than it does with 39+11 CS, etc.
Weaponskill: Goes up with +'s over 50 just as much (or even more) as an individual train in it.
Damage Variance: The jury is still out on exactly how much it lowers your variance, but I think we all find that the returns are diminished above 50. Still, if you were to attack unstyled for 100 rounds at 50+11 weapon spec, and then did it again with 39+11, the former would have a higher average hit. (it may be a small difference, however)
Stealth: Previously, Stealth was one of the few skills that did almost nothing over 50. ToA changed that. Cougar (former NS TL, providing his last official feedback to the Shade boards) revealed to us that the new ToA items that increase the users ability to detect stealthers can be combatted by the stealther for having stealth skill >50. So an assassin with 35+15 stealth (and no increased stealth ToA items) will be seen easier by people with an increased stealth detection ToA item (those without these items will see stealthers as they do now) compared to a Stealther with 40+15+ToA items, for instance.
Dual Weild: Has absolutely no degradation in effectivness as it surpasses 50. It increases by .68% every train, whether training/adding bonuses from 1 to 2, from 39 to 40, from 50 to 51 or 69 to 70.
There is only one skill that does nothing for assassins who specced it over 50, and that is Envenom. And I wouldn't be surprised if ToA changed that too, but I guess we would have heard about it by now if it were true.