Well, the most you need to balance is Granted Power vs. Granted Spells, for the most part. Even the "good" domains in the PHB you can, by the rules, mix and match as you like if you want (Strength and War, for instance), but those have either rather unimpressive spells (Strength gives you some Bigby fun at higher levels, but the hand spells are rather unimpressive for their level in general), or mediocre granted powers (Taking the War domain is like taking a level of fighter that sucks).
As a general rule, you can include as a granted power something that's about equal to two general feats as long as the domain spells only use Cleric spells, and don't use any earlier levels. If you weaken the granted power a bit (to about the power of one feat), feel free to poach from others' spell lists, but don't change the levels (or even give them a level higher), and don't make them the signature spells of other classes(there's a reason a Fire cleric doesn't have Fireball, after all).
To be careful, check the domain's power against what a normal cleric with the domains from the PHB is capable of -- if your domain seems like it is very appealing to choose, it's probably too potent.
I guess that's not extremely helpful, but it's some rough guidelines. ^_^;
It's a 'problem domain' because it makes it virtually impossible to capture, chase, or contain the PC -- they have to *want* to be where they are. 
