Bukkit

Since version 4.9.2+, an event has been supplied by PlayerHeads named HeadRollEvent which contains information about the droprate and droproll and expected head drop success. By capturing this event you can modify droprates and success as you please.  By default, drops succeeds if the "roll" value is within (below) the droprate value - the value you set of the success controls whether a head will be dropped.

Note: "Effective" values indicate values that already have inbuilt modifiers applied to them, while "original" values rely on configured rates.

Changing droprates (4.9.2+)

Modification in early versions relies mostly on setting the success value of the event, however it's possible to read the original and effect dropRate/dropRoll values, as well as modifiers like with the method getLootingModifier, which can allow you to make an informed decision about the success.

The below example modifies the droprate of all heads with a 5% proportional buff.

@EventHandler
public void onRoll(HeadRollEvent event){
 double dropRoll = event.getEffectiveDropRoll();
 double dropRate = event.getEffectiveDropRate();
 double newDropRate = droprate * (1 + 0.05); //increase the droprate by 5% of the existing rate
 event.setSuccess( dropRoll < newDropRate ); //update the succcess of the event
}

Changing Droprates (5.2.16+, 5.3)

In 5.2.16 and higher, it is be possible to both indicate changes in the 'effective' values by your plugin, as well as to register your own modifiers and recalculate the droprate without upsetting other plugins.

In addition to having access to setEffectiveDropRate you now can access setCustomModifier which will make modifying droprates much easier.  Other methods are available for accessing or retrieving all the modifiers affecting an event.

A description of the Types of modifiers available here.

The following example also applies a 5% proportional buff to all head drops, but allows other plugins to know about it and not override your modifier by accident.

DropRateModifier modifier = new DropRateModifier(DropRateModifierType.ADD_MULTIPLE, 0.05); 
@EventHandler
public void onRoll(HeadRollEvent event){
 event.setCustomModifier(yourPlugin, "mybuff", modifier);//register your named modifier
 event.recalculateSuccess();//update the effective droprate and determine success
}

 If you would like to apply your your modifier but not update the success (to test, perhaps), you can also use the applyModifiers() method.

Changing Droprates (5.2.17+)

5.2.17 and higher offer a simplified method of adding modifiers and updating the success:

DropRateModifier modifier = new DropRateModifier(DropRateModifierType.ADD_MULTIPLE, 0.05); 
@EventHandler
public void onRoll(HeadRollEvent event){
 event.setCustomModifier(yourPlugin, "mybuff", modifier, true);//register your named modifier and apply it
}