A home stage is a stage or set of stages associated with a character by certain game modes.
Characters' home stages are normally from the same universe as the character. However, in all the Super Smash Bros. games there are playable characters who do not have a stage belonging to their universe; such characters are instead assigned a home stage from another universe.
Super Smash Bros.
Each of the eight starter characters has their own home stage, while the four unlockable characters share stages with starter characters. All starter characters and two of the unlockable characters (that being Jigglypuff and Luigi) have home stages from their own universes. The two home stages they have is Saffron City and Peach's Castle. The other two unlockable characters (Captain Falcon and Ness) have home stages (Planet Zebes and Dream Land) from different universes as they are fought there in their unlockable character battles, due to there being no stages from their own universes (F-Zero and EarthBound, respectively). Those two stages Planet Zebes and Dream Land is likely considered Captain Falcon and Ness's (due to those two stages being fought on when unlocking them).
Mushroom Kingdom an unlockable stage (a stage from the Mario universe) is not the home stage of any character; although it's likely considered Mario and Luigi's. However, even if the stage is unlocked, Stage 2 of 1P Game still takes place on Peach's Castle.
Super Smash Bros. Melee
In Super Smash Bros. Melee, characters have different home stages in different game modes. All characters have a home stage for All-Star Mode, most have one or two home stages for Classic Mode, and unlockable characters have a stage for their unlock challenge fight.
All universes with playable characters have at least one stage, except Fire Emblem. However, even for characters that have a stage from the same universe, in some game modes they will use a stage from a different universe as their home stage. The said song from the Fire Emblem universe however can play on Temple as alternate music and is selectable for a playable stage on VS. Mode. So this stage is likely considered Marth and Roy's.
Super Smash Bros. Brawl
All characters' home stages are all of the Brawl stages from their own universe (Melee stages are not used as home stages), with the exception of R.O.B. and the stage Mario Bros. There are no stages from R.O.B.'s universe, so he instead has Mario Bros. as his home stage (although it's likely considered R.O.B's home stage; as it is not available as a home stage for the Mario universe).
Super Smash Bros. 4
Unlike in previous games, Past Stages also serve as home stages. All characters' home stages are all of the stages from their own universe, unless there are no stages from their own universe. Characters from universes without stages have all of the stages whose universes lack characters as their home stages. The Mii Fighters' home stage is considered to be Battlefield, as they are part of the Super Smash Bros. universe and are only fought in Classic Mode as enemy teams.
Super Smash Bros. Ultimate
In Super Smash Bros. Ultimate, home stages are heavily downplayed from their past appearances, due to Classic Mode setting a single stage for each fight instead of randomly by character, and All Star Mode allowing the player to choose the stage.
Hypothesis of "home advantage"
There is no clear or consistent benefit to a character fighting on their "home stage." Any advantages that certain characters have over others on stages happen across the entire stage list and are situational; they are not affected by the universes in which the characters originate from (for example, Fox and Pikachu dominate on Temple, even though they do not originate from the Zelda universe). In some cases, it may be to a character's disadvantage to be fighting on their home stage; for example, Ness is unable to use his recovery move when knocked between buildings in Fourside. Additionally, Final Destination, which acts as the home stage for Roy, is disadvantageous for him against nearly every character (except for arguably Fox and Falco) as he is much more vulnerable to combos without any platforms to escape to. In Brawl, the ledges of the Lylat Cruise stage are thinner than most other stages, causing Fox, Falco, and most notably Wolf to curve underneath the stage more frequently when using their respective recovery moves instead of directly grabbing the edge. Additionally, in Skyworld, Pit's Centurions in his Final Smash will crash into the breakable platforms when they aim for opponents, quickly destroying the stage and temporarily removing all ledges; this consequently removes Pit's ability to plank and makes him much easier to gimp.
However, in contrast, some stages do offer advantages to some characters; as mentioned before, any such advantages are non-circumstantial, but these certain stages may have been the origination for the "home advantage" hypothesis. In Melee, Fountain of Dreams serves as Marth's home stage, and is frequently cited as one of his best stages in the entire game, even at high-level tournament play. The stage's small size allows him to control space more efficiently, and the extended bottom blast line allows him more room to recover with Dolphin Slash, which travels purely vertically. In Brawl, on Bridge of Eldin, Zelda and Sheik's Light Arrow, Ganondorf's Beast Ganon, and Toon Link and Link's Triforce Slash are much easier to use, and harder to dodge; the frequent absence of a lower blast-line also acts as a benefit to Link, Ganondorf, and Sheik, who normally have relatively poor recoveries. The low blastline of Shadow Moses Island acts as a benefit to Snake, as most of his attacks (especially his special moves) have mostly upward knockback; his high weight and falling speed make him more resistant to vertical KOs, so he is not as affected.
On other stages, characters can receive neither a clear advantage nor disadvantage. On Summit, for instance, all the characters slide around, except for the Ice Climbers, who experience no change in their friction when walking on the stage. Like other characters, however, they are still unable to grab onto the ledges in the stage; this trait causes Belay to more frequently cause Nana to be KO'd, thanks to Belay giving Popo more height than Nana when there is no ledge to tether to. Another example is Little Mac on Boxing Ring: the stage gives no access to the bottom blast line, which remedies Mac's poor recovery, but also has plenty of verticality, making it difficult for him to traverse the stage. In Super Smash Bros. 4, the Ω form of Boxing Ring takes this even further in Mac's favor — while being based off of Final Destination means it has a lower blast line, the walls of the actual stage reach all the way down to it, allowing Mac to make full use of his uncharacteristically superb wall jump.