I'm planning on playin an Eberron campaing, starting early next year. So since the campaign setting is not out yet, I tought a bit on how to implement dragonmark.
Here is what i've come up with so far :
One feat to make you a member of a particular House, give you skill training or skill focus in a skill realated to the house (basically it is the same as skill training or skill focus, just with a different flavor, and that you can be part of only one House)
then three utility power swap feat
Some of the ability given by dragonmarks are already implemented as utility power (cure light wounds, expeditous retreat, dimension door, etc...), so for these it's easy.
If the ability is now a ritual, you can make the power to allow to perform the ritual at reduced cost/reduced preparation time/increased efficiency (bonus to skill check). You can make the power at will/encounter/daily and combine any of the three bonus to balance it.
If the ability doesn't exist yet in the core books, well you'll have to work a bit more to create the power...
least dragonmark (requires to be a memeber of the associated House, heroic tier) :
swap you're second level utility power.
lesser dragonmark (require least dragonmark, heroic tier)
swap you're 6th or 10th level utility power (depending on the power gained)
greater dragonmark (requires lesser dragonmark, paragon tier)
swap you're 16th or 22nd level utility (again depend on the power gained)
You can take the feat before level 22nd and wait for 22nd level to swap you're utility if you want to qualify for Sibery Mark epic destiny
And finally Sibery Mark would be an epic destiny requiring greater dragonmark and give a 25th level utility power (+ other benefit to determine)
I think it should be pretty balanced, since the feats don't grant you any power, just increase your choice of utilities.
It can help to fill missing roles in a party (for instance a party who doesn't have a lot of access to healing power, could have someone bear a least dragonmark of Healing for cure light wound...)
The hard part is to convert the ability (well it depends, cure light wound is easy to convert for instance

You don't have to convert everything though, just convert the one you will really use. And you can even come up with new power that fit the flavor of a particular mark
If you get the chance to try it before me, lmk how it plays.
Cheers