They've been defined by Maddie as an "odd manifestation of ectoplasmic energy and post-human consciousness". However, some ghosts in Danny Phantom are not dead people, this could mean that human don't really know what they are.
As stated above, Butch Hartman has said that they're "monsters/creatures" from a mysterious dimension and not dead people. However, there are contradictions with this statement and the ones given in the series and by the producers about the origins of other ghosts as well as Maddie's definition of ghosts.
For instance, Desiree is stated to be a harem girl when she was alive whose heart was broken and after her death she'd spend eternity granting people's wishes. Ember was said to be an unpopular high school-aged girl who had large dreams of becoming a rock star and died when her house mysteriously caught fire (these facts seem to reflect on her musical lyrics). Sidney Poindexter is clearly presented as nerdy teenager who lived in the 1950s, when he studied in Casper High and suffered from severe bullying there. It is also implied that the Lunch Lady Ghost worked in Casper High when she was alive, as she gets disturbed when the cafeteria menu is changed. Hotep-Ra is shown as the spirit of an ancient minion of the Tucker Foley look-alike King Duulaman. The Dairy King used to live in Vlad's mansion when he was alive. The starting dialogue in "Public Enemies" also implies that ghosts are dead people. Additionally, the terms "malevolents spirits", "spirits"  and "afterlife"  have often been used when referring to ghosts.
These two concepts makes the ghosts' true nature ambiguous at best.
Ghosts are spectral entities capable of going in-between the Ghost Zone and Earth through portals that open and close at various times and in various places.
In the series there are several indication that a ghost is the spirit or a death person and it is proved that they can breed.
Some other ghosts like Clockwork or the Observants, are entities of a supernatural nature and weren't from earth originally, but some are reminiscent of Anthropomorphic Personification (human-like) in nature and others like Pandora were the inspiration for ancient nature spirits/gods and characters in mythology and folklore; like:
- Pandora (who is famous in Greek Mythology for Pandora's Box). Along with Pandora; Medusa, Argus Panoptes, Cerberus and Centaurs, minotaurs, unicorns, Hydra, Pegasus and Cyclops, which are all seen in Boxed Up Fury.
- Wulf - a 'ghost' whose physical appearance is that of a Werewolf - a monster of medieval European, Native American, Nordic and folklore among other cultures.
- Nocturne - the 'ghost' of sleep and dreams who is reminiscent of Hypnos (sleep), Morpheus (dreams) and Phobetor (nightmares). Nocturne's physical appearance links him as an embodiment of the night.
- The Fright Knight - a 'ghost' with the appearance of a medieval knight who is also known as "The Spirit of Halloween"; the Fright Knight's main power is contained within his sword "The Soul Shredder" which when it cuts it victim will send them into an alternate pocket dimension were the victim's worst fears and nightmares come true.
Characteristics, Abilities and Life Span
- All ghosts seem to possess standard powers (flight, invisibility, intangibility, over shadowing etc). Although some ghost appear not to, they may just not be using them. Other powers that are rarer (although still common) include duplication, ghost rays and superhuman physical abilities (strength, stamina, durability, agility). There are also even rarer powers, like pyrokinesis, telekinesis, cryokinesis, etc, which very few ghosts have. Some ghost even have individual powers, which seem to have something to do with what they did or what they were into when they were alive; for example Technus was a scientist in his life and he can control all machines and act like a computer program. The exact rules behind this are never revealed though, what exactly makes some ghosts so powerful is unclear.
- The similarities between ghosts and humans ofter vary. Some ghosts are very similar to humans, not only in appearence, but also in rationality — most of the main villains in the series (Ember, Youngblood, Walker, Desiree, the Box Ghost, etc) have these characteristics. Some of them do not exactly look like humans, but are still humanoid and are perfectly rational, especially the ones introduced later in the series (like Undergrowth, Vortex and Nocturne). Some, possibly most, however, are irrational monsters or animals, and mostly appear in short scenes or as cameos (such as the Ectopuses, the Ghost Snake and the Ghost Wolf). Some ghosts, while not similar to humans in appearence, have rational minds; sometimes they are shapless blobs (such as Skulker or Bertrand in their true forms) or anthropomorphic animals (such as Youngblood's assistant and the Vulture Ghosts). Some also seem to be partially rational, such as Shadow, who diplays almost no personality and doesn't even speak, but displays joy when wrecking havoc and seems to comprehend Johnny 13's commands; and Wulf, who, despite following his animal instincts, is able to speak, feel and think.
- The name for ghosts have different origins. Some ghosts, like Sidney Poindexter, retain the names from when they were alive. Other ghosts seem to choose their own names. For example, Youngblood claims that he calls himself Youngblood, which may indicate that he has another actual name, yet the chosen name is how all of the other characters (including ghosts) call him. Some ghosts have common human names, or are named by surnames or nicknames (Lydia, Penelope, Bertrand, Walker, Johnny, Kitty). Some don't have human given names, instead being named after their powers, abilities and/or characteristics (Amorpho, Vortex, Ember, Skulker, Fright Knight, Frostbite, Clockwork). Some of the names are just a literal explanation of what the ghosts are (Box Ghost, Lunch Lady Ghost, Ghost Writer, The Vulture Ghosts, Shadow).
- Most of the ghosts in the show have very strong obsessions with something, which may lead into evil behaviors. The Lunch Lady Ghosts is excessively conservative about the Casper High cafeteria menu, Penelope Spectra is obsessed with her appearence, Walker is extremely strict with his rules, Klemper has a deep necessity of having friends, Undergrowth is irrational about the superiority of plants and hatred towards humans, Technus is exaggeratedly proud of his self-proclaimed "master of technology" status and wishful of using that for world domination, Youngblood has a harsh grudge against adults, and so on. These obsessions are commonly related to the ghosts' powers. These explanations are possibly related to the ghosts' previous lifes, though that is hardly ever explained. There are some exceptions, such as Sidney Poindexter, who hates bullies extremely because he constantly suffered with them during his time as a high school studant; and Desiree, who is obsessed with granting wishes (to the point of not being able to stop herself from doing it), consequence of having her heart broken by a Sultan, who has previously promised to grant all of her heart's desires when she was alive as a Harem girl.
- Despite being ghosts, it appears that (at least while in the Ghost Zone) they can still do many things that living things do (eat, sleep, wash etc). Several of them act like beings do when they are alive, although seeing as very few ghosts have ever had their lives before they died revealed, whether they're acting like they did when they were alive is unknown.
- Several ghosts are motivated by things that happened in their life, which causes them to act the way they do in their afterlife. For example Desiree, during her life, was promised her heart's desire only to lose it. In her death, she goes around granting wishes, only not in the way that one would want them.
- A topic that could be subject of a small debate among fans, is whether ghosts have lifespans, and if they do, how do they work. Due to the fact they are obviously not alive, it seems likely they don't have lifespans, which means, among other things, that they don't age. This seems to be supported by evidence given in the series, one example being Sidney Poindexter, who although he is shown to have died in the fifties (which would make him at least 60 if he were alive), still looks like he did when he died (14-17). Additionally, Princess Dorathea and Prince Aragon are over 1600 years old according to the princess' own statement in Beauty Marked, but they don't have eldery appearances (though this could be because of the Amulet of Aragon or because they lived in a part of the Ghost Zone where time didn't flow). Another example is Desiree, as the scenery and manner of dress shown in her backstory seem to indicate that she is well over a hundred years old, but despite this she retains a youthful body. Another possible example is Ember, who from the way she acts and talks, seems likely to have been alive during the seventies or eighties, and still looks like she is in her late teens. However, while these examples (along with other information) suggests that they don't age, in The Ultimate Enemy when Danny was in the future, all the ghosts he met looked older (but this could be because they had let themselves go after being beaten by Dark Danny). Penelope Spectra is a different case: while she seems to age, she can absorb people's misery to keep her youthful appearance (and it is implied that Bertrand can do that too).
- Another debatable topic about their lifespans is the question of their mortality. Although it is often acknowledged that they are dead, several times it's implied that they can still be killed. Perhaps the best example of this is in Prisoners of Love, when Walker states three times in the same sentence that he can be their executioner, his speech to Danny at the end also seems to imply that they still can be killed. This has caused some to speculate that maybe the relationship between the Earth and The Ghost Zone might be like the Celtic beliefs in death (that when you die you go to another world, but you can die in that world and when you do you go back to earth) or that there might be another zone, where the ghosts who die in the ghost zone go. However, it is far more likely they either meant that, seeing as ghosts are technically made of something, what they're made of can be destroyed, or they can be injured to a state where they are incredibly close to death. This is, however, entirely speculation. If formerly Human ghosts are 'echoes' that have "refused to move on" for whatever reason, it may be possible to force them out of this state and into a "true afterlife".
- A final question heavily connected with the two above is how long they can live for, though like the others unanswered this has never been answered, nor, perhaps, can it be answered without the two above being answered first.
There are at least three known weaknesses that all ghosts share:
Ectoplasm and Ectoplasmic Energy
Some of the weaponry designed and built by ghost hunters, like the senior Fentons, utilise Ectoplasm and Ectoplasmic energy against ghosts (see: List of Fenton Works products). Then again, ghosts themselves are made of ectoplasm and ectoplasmic energy, and tend to use both for their abilities as well.
Seen in "Infinite Realms", Blood Blossoms are blood-red flowers with anti-supernatural properties and were used by John Fenton Nightingale (an ancestor of the modern Fentons.) Blood Blossoms were used to great effect against witches and ghosts/spirits when in their presence--rendering them not only powerless, but would have ghosts and familiar spirits withering in agony until the flowers were removed. Vlad referred to them as "a primitive Spectre Deflector"-- (which are only effective on physical contact). Blood Blossoms are also edible, they are seen as an excellent garnish in sandwiches. Once Blood Blossoms have been ingested (chewed, swallowed and deposited in the stomach) it can no-longer affect a ghost. Blood Blossoms are to the supernatural as Kryptonite is to Superman - but while Superman was spared from the effects of Kryptonite when it was locked up in a lead container - a ghost/spirit/witch is safe from Blood Blossoms if the flowers are simply consumed by a normal human/animal.
The "unique anti-ghost element... (its) negative effects can only be felt by ghosts." Unlike Blood Blossoms, ghosts can merely be in the presence of ectoranium and feel no effects--its only when they come into physical contact with ectoranium that they are shocked by the opposing energies--which is why it is known as the "anti-ghost element"--so no ghost can touch it; Ghosts can phase themselves through ectoranium--but they cannot touch it or phase it through solid matter (as seen and mentioned only in Phantom Planet.)