The 1st-level Sor/Wiz spell ebon eyes [trans] (Spell Compendium 77) is a confusing mess, because, as written, it does allow the affected creature to see through natural and magical darkness. As the core rules place an otherwise high premium on the ability to see without a light source through natural darkness and even higher premium on the ability to see through magical darkness, it seems strange that a 1st-level spell should obviate both, but the spell ebon eyes does, and the spell does so apparently to the limit of the affected creature's normal vision.
"So ebon eyes is awesome?"
As written, yes. While there are many ways of gaining darkvision, gaining darkvision to the limits of normal sight is otherwise the sole the province of the obscure 4th-level Sor/Wiz spell superior darkvision [trans] (Unapproachable East 53). And while there are a handful of ways of gaining the ability to see through magical darkness, only the equally obscure 7th-level Sor/Wiz spell fiendish clarity [div] (Fiendish Codex I 94) allows seeing through magical darkness as if it were normal darkness, hence to the limit of the affected creature's darkvision (yet the spell itself only provides, among other effects, darkvision 60 ft.). For further comparison, the 3rd-level Fiendish Codex II spell devil's eye and the spell true seeing only allow seeing through normal and magical darkness out to, respectively, 30 ft. and 120 ft. Further, note that these spells are the best ways of almost duplicating the effects of the spell ebon eyes; domains, feats, and magic items are, objectively, worse at the task.
This makes the 1st-level spell ebon eyes the best see-in-the-dark spell printed for Dungeons and Dragons 3.5.
For a more conservative approach to seeing in the dark
It's true that the game overvalues the ability to see in the dark without a light source, and it's true that the game overvalues the ability to see in magical darkness. However, just because such abilities are overvalued doesn't change their values.
Thus a conservative DM may view the spell ebon eyes as, perhaps, a little unbalanced.1 For such a cautious DM, below are two options.
Consider using the original version of the spell ebon eyes...
When the spell appeared in the Dragon #322 article "Patterns of Shadows and Light: Same Coin, Different Sides" by Jason Nelson, it looked like this:
Level: Assassin 2, Clr 2, Sor/Wiz 2
Components: V, S, M
Casting Time: 1 standard action
Target: Creature touched
Duration: 10 min./level
Saving Throw: None
Spell Resistance: Yes (harmless)
The subject of this spell gains the ability to see normally in magical darkness and magical shadowy condition [sic], although it [the spell] does not otherwise improved the subject's ability to see in natural dark or shadowy conditions. While the spell is in effect, a jet-black film covers the subject's eyes, a visual effect that gives the spell its name.
Material Components: A pinch of powdered black gemstone of any type.
In other words, the Dragon magazine version is a low-level spell that grants the subject the ability to see normally only through magical darkness, to the limits of the affected creature's own vision. For example, in an area of magical darkness that's also naturally dark, a creature affected by the spell ebon eyes that lacks darkvision still can't see without a light source, but a creature possessing darkvision can see to the limits of its darkvision.
...Or just changing the first natural to unnatural
As written, the full Spell Compendium description of ebon eyes is, honestly, borderline gibberish, but change the first natural to unnatural and the spell's effect is a bit clearer:
The subject of this spell gains the ability to see normally in unnatural and magical darkness, although it does not otherwise improve the subject’s ability to see in natural dark or shadowy conditions. The subject ignores the miss chance due to lack of illumination other than total darkness.
Emphasis mine. A conservative DM could do worse than make this minor change.
1 Such a DM should, however, note that only the most unusual campaigns will be ruined by allowing such a low-level see-in-any-darkness spell. For example, in the core rules, even a low-level party can pay a 20th-level spellcaster 1,850 gp to cast on an object continual flame heightened to a 9th-level spell therefore eliminating most worries about magical darkness unless the object's specifically targeted by other effects.