<GlobalInterColonyMods>
<EffectType>Maintenance</EffectType>
<Target>
<TargetType>Colony</TargetType>
<TargetQualifier>NotPatriotic</TargetQualifier>
</Target>
<BonusType>Flat</BonusType>
<Value>0.02</Value>
</GlobalInterColonyMods>
The above will increase the maintenance costs of everything built upon every colony you own by (number of inhabited planets in your empire)*2%. If you were to use <BonusType>Flat</BonusType>, each colony's maintenance would be increased by 0.02 credits per inhabited planet in your empire. You could change the magnitude of the effect by modifying <Value>0.02</Value> to something else.
Alternatively, you could take this
<GlobalColonyMods>
<EffectType>Growth</EffectType>
<Target>
<TargetType>Colony</TargetType>
</Target>
<BonusType>Flat</BonusType>
<Value>0.1</Value>
</GlobalColonyMods>
and change the effect type to Maintenance and change the bonus type and value if you so desired; this leaves the per-colony maintenance cost independent of the number of inhabited worlds in your empire and is effectively the same as adding a maintenance cost to the Colony Capital. I've never tried using an effect type of maintenance for GlobalColonyMods, but I see no reason why it shouldn't work.
(This, incidentally, is how the game sets the base population growth, which is where the above came from, base planetary defense, base resistance, and the sponsor decay.)
There is a possibility that you'll need to include these in GalCiv3GlobalDefs.XML; I haven't tried using GlobalColonyMods or GlobalInterColonyMods outside of that file, but I don't know of a reason why it wouldn't work since you're not overwriting anything already defined in the file.