For each holding over your desmene limit you will suffer penalties :

- Your vassals' opinion of you will drop (apparently by 10 for **each** holding over the limit, I experienced huge penalties myself after winning the crusade and conquering Jerusalem). I think that it takes 1/2 months before applying this penalty.
- An income tax penalty (wikia say -12.5% for **each** holding over the limit)
- A bunch of bad events related to your holdings.

Remember that having a bit more holdings is not always bad : you ensure that your vassals are under control (because you raise way more levies) and if you don't go too high, you usually make more money through direct taxes than from feudal taxes.