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:
Ebon Eyes
Transmutation
Level: Assassin 2, Clr 2, Sor/Wiz 2
Components: V, S, M
Casting Time: 1 standard action
Range: Touch
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.
Best Answer
A spell is called a spell and listed in a spell list
Something that is a spell will be listed in such a way that indicates it is a spell.
Or, as Jeremy Crawford says here:
If you find something and are unsure if it is a spell, first see if there is anything in the description that says it is a spell. If it says that you "cast" it, or that it has a "spell level", or if it is listed under the Spellcasting, Innate Spellcasting or Psionic Spellcasting header in a stat block then it is a spell.1
If there is nothing indicating it is a spell there, look up the name of the ability in question in the resources below. If it's not listed there, it's not a spell. If it is listed there, it is.
Spell lists can be found in the books or online
All spells currently released are listed in the Player's Handbook (Chapter 11), Xanathar's Guide to Everything (Chapter 3), or Elemental Evil Player's Companion (Chapter 2). Each of these chapters is simply called "Spells". The Sword Coast Adventurer's Guide also contains 4 cantrips for sorcerers, warlocks, and wizards; they are listed at the end of the list of classes on p. 142-143.
You can find all the spells compiled into one list on DnDBeyond here.
Examples:
"Spell-like" abilities are not spells
Some abilities look very similar to spells, but if they aren't in a spell list, they aren't spells.
The beholder has the ability Eye Rays with different effects. One of which is:
"Charm Ray" is not found in any of the spell lists nor does anything in the description say it is a spell and thus it is not a spell. It also does not allow for the casting of spells. Thus, we must conclude that "Charm Ray" is not a spell. As such, anything that affects spells will not affect it.
Abilities that allow the casting/effects of spells are not spells (but the spells resulting from them are)
Other abilities let you cast spells. These abilities are not spells in and of themselves, they just allow you to cast spells.
For example, let's look at this Way of the Four Elements Monk ability:
We can determine that the ability flames of the phoenix is not itself a spell by looking up its name in the list of spells. It isn't there therefore it is not a spell. However, the ability description has several clues that tell you that it does involve the casting of the spell. Firstly, it says "cast [name]". Since casting is something that is only done with spells this is going to be a spell. And if you look up fireball in the list of spells you will find it there. Thus, fireball is a spell cast from the ability Flames of the Phoenix which is not a spell. The fireball will be affected by anything an applicable fireball cast by any other method would be.
The same thing applies to something like a potion of heroism which says:
The potion is not considered a spell (there is no spell called "potion of heroism" in the spell lists) but it has a spell effect in it. So, you are considered to be under the effects of that spell for all purposes including dispel magic (see this Q&A for more on that).
Something like the potion of water breathing (though also not a spell itself for the same reasons) does not result in a spell being created because nowhere in the description is a spell name listed.
Thanks @Ruse for giving me feedback and advice in putting this together.
1 - One thing to note is that the phrase "spell slot" is not indicative of being a spell. There are many abilities that use spell slots that are not spells (in addition to spells that don't use a spell slot at all). Crawford explicitly says this in this tweet about Divine smite, for example:
Thus, even if something uses a spell slot or says "spell slot", that is not enough to determine if it is a spell. In this case, simply look up the name of the ability and see if it is in a spell list. That will tell you for sure.