Holy and Unholy Ground
Yes, rules for these kinds of sites already exist, most notably under the spells “Hallow” and “Unhallow.” However, if you want to make an unholy dungeon new and unique, or if you simply do not like the existing rules on the subject, you might want to try these alterations.
Unholy or holy ground of this type comes in four ranks, to make it usable to DMs who are running any level of adventure. These ranks are numbered one through four, and have increasingly dangerous effects on the players. Adding unholy or holy ground to a dungeon also increases the challenge rating of all encounters within the area, by rank. Level one holy or unholy ground does not increase the challenge rating, level two increases the challenge rating by one, level three increases the challenge rating by two, and level four increases the challenge rating by three.
First, unholy or holy ground is filled with energy of the appropriate type, and it immediate seeks to squash energy of the opposite nature. All clerics of the opposite moral alignment (good for unholy ground, evil for holy ground) cast there spells at a reduced caster level, equal to the rank of the ground. Similarly, clerics of the identical moral alignment can harness the energy that is present, and focus it into their spells, giving them an additional caster level equal to the rank of the ground. Spells of the opposite moral alignment, and healing spells (including Heal) for unholy ground and inflict spells (including Harm) for holy ground, require a concentration check (DC 14+2(rank of the ground)) to cast. If the ground is of the fourth rank, casters that fail this concentration check are in an especially bad situation. The reverse effect of the spell is flung at them, as though the cleric had cast it himself (so inflict spells instead of cure spells, and harm instead of heal.)
Creatures summoned by clerics of the same moral alignment of the ground have an increased duration, depending on the rank. Levels one through three increases the duration by one round per a rank, and level four doubles the duration of these spells. Clerics of the opposite alignment suffer the reverse effect, losing one round for summoned creature per a rank of the ground and losing half of the duration for level four (if the creature would stay for less than four rounds, it simply cannot enter.) Furthermore, summoned creature of the opposite moral alignment of the ground must make a will save every round (DC 14+2(rank of the ground)) or be banished back to where they came from.
Paladins and Blackguards suffer a penalty to all saving throws while on ground of the opposite alignment equal to the ground’s rank.
Finally, undead gain turn resistance equal to the rank of the unholy ground. In the case of holy ground, undead are considered to be one hit dice less for the purposes of turning them.
Please note that this will only be a really interesting mechanic for parties who are decidedly one moral alignment or the other, or at least have several members who rely on holy magic. Also note that a ground can lose its holiness or unholiness, through blessing, for unholy ground, or sacrificing living creatures, for holy ground.