"Happy indeed will you be if he finds you faithful in your stewardship. You are called shepherds; see that you do not act as hirelings. But be true shepherds, with your crooks always in your hands. Do not go to sleep, but guard on all sides the flock committed to you. For if through your carelessness or negligence a wolf carries away one of your sheep, you will surely lose the reward laid up for you with God."
- - Pope Urban II.
Chaplains were originally formed by Lorgar as part of the religious slant he brought to the Word Bearers, charging them with spreading the cult of the Lectitio Divinatus, his early form of Emperor-worship. After assuming control of the Council of Terra, Malcador the Sigillite instructed the Space Marine Legions to employ Chaplains to enforce the Decree of Nikea, the Emperor's restrictions on Librarians, as a sort of proto-Commissar.
In the present, a Chaplain's role in a chapter is to root out heresy, inspire other Marines by chanting a litany of verses, maintain the Chapter's relics and traditions, and basically make the Marines around him righteously angry. Unlike Commissars of the Imperial Guard, he isn't keen on executing his own men for simple cowardice, mainly because Space Marines only retreat to gain a better tactical advantage and the fact that a Marine is more expensive to create than an expendable guardsman (plus the whole "And they shall know no fear"); but he does still torture/kill xenos, mutants and heretics for tactical, religious, or recreational purposes. Chaplains are an HQ unit and use a Crozius Arcanum. It is their badge of office, a fuckhueg energy-wreathed mace capable of going straight through armour and utterly shattering your head right off of your shoulders in a single swipe. All the while looking totally sweet in his black Power Armour and skull visage helmet while scaring the living shit out of the enemy (Well, in fluff. On the tabletop it's just a Power Mace in 8th ed.), higher ranked Chaplains may also be issued Terminator armour. Outside of the company Chaplains, you have the Master of Sanctity or High Chaplain oversees the Chapter Chaplaincy and is a senior advisor to the Chapter Master, and the Reclusiarch, who oversees the Reclusiam, where the Chapter's sacred relics and trophies are displayed. Many Chapters combine the two posts, but not always.
For all intents and purposes, just imagine a Space Marine, but even more fanatical and badass. He also has great oratorical skills to make his brothers stop bitching and to pick up his knife then charge that Bloodthirster and stab him right in the balls because goddammit that's how you make the Emprah proud. It is also suggested that Chaplains use their "oratory" skills for other purposes as well, but these may just be rumours spread to question the MANLINESS of the Spess Mehreens. As an interesting aside chaplains seem to be more in-touch with their emotions than other Space Marines, seriously though if you listen to their lines in Dawn of War they sound like they're about to burst into manly tears of pride or rage; they must watch Fist of the North Star as part of training.
The Chaos Space Marine equivalent is the Dark Apostle, most associated with the Word Bearers. Older fluff stated that only Word Bearers could have them because no other Chaplains ever fell or will fall to Chaos... which later editions revealed to be a lie, since Chaplains in their present form only originally existed in the Word Bearers in the first place. (They did start to appear in other Legions after the Edict of Nikaea though. And that's not counting more recent Chapters going renegade.)
Blood Angels Chaplain
The Blood Angels Chaplains were originally known as "Wardens", who served as advisors and mentors to the younger generations. When the Edict of Nikaea was declared and the Chaplain Edict followed, the Wardens were appointed to oversee enforcement. Following the Horus Heresy, the Wardens of the Blood Angels and their successor Chapters became Chaplains, and were tasked with an additional, somber purpose: they were to lead the Death Company, those Marines who fell to the Black Rage and the Red Thirst, into battle. Being surrounded by raging berserkers, the Chaplains must have iron strong wills to oversee these Marines and maintain their own sanity.
Dark Angels Interrogator-Chaplain
The Dark Angels and their successors have an extra rank for Chaplains who make it into the Inner Circle and learn the "truth" (or at least part of it) about the Fallen Angels. After passing several trials of the soul (the penalty for failure being death or worse), they interrogate (read: torture) captured Fallen Angels to try and force them to repent for their crimes. These "Interrogator-Chaplains" are extremely patient and resilient against the *cough* insidious lies of captured heretics, and will take as long as necessary to finally break them. To put this in perspective, the very best Interrogator-Chaplain that the Dark Angels ever had only managed to get ten Fallen to confess and repent over the course of 300 years of service.
Iron Hands Iron Father
Among the Iron Hands, the Chaplains are known as an "Iron Father", which combines the role of Chaplain and Techmarine together, which reflects the Iron Hands heavy preference for augmentics. Also unique in the fact that they're completely separated from the Ecclesiarchy altogether, considering the chapter's predilection towards machinery and the like. The spat ended with them splitting off and the Iron Hands unable to have Rosarii. To compensate that, the Iron Hands have to fabricate their own equivalents using some special Adeptus Mechanicus schemes. Needless to say, when comparing the technological prowess of the Ecchlesiarchy and the Mechanicus...
Space Wolves Wolf Priest
The Chaplains of the Space Wolves are the Wolf Priests, who combine the role of Chaplain and medic into one. All Wolf Priests, along with the Rune Priests (Librarians) and Iron Priests (Techmarines) serve as part of the Company of the Great Wolf (the elite Great Company under the Chapter Master of the Space Wolves) and are assigned to the other eleven Great Companies as needed.
Grey Knights Chaplains
Believe it or not, Grey Knights do have Chaplains of their own. The Chaplains of The Emperor's Space Paladins don't differ greatly when compared to other Chapters, but the challenges Grey Knight Chaplains have are unique (and very often difficult). Although Grey Knights are incorruptible, with time even their faith can be tested and doubt will assail their minds at some point one way or another. Chaplains are here to straighten them up, get them on the proper tracts, have their doubts evaporated and give new meanings to the mission of their Battle-Brothers. Just like all Grey Knights, the Chapter's Chaplains are also Psykers. Also were known to not be available as HQ options for some stupid reason until 8th.
- Varnus: An Ultramarines Chaplain whose defining deed (making him a potential mary sue (IT WAS AWESOME NONETHELESS)) is single-handedly pwning a fuck-mothering BLOODTHIRSTER. Needless to say, Khorne was very salty.
- Asmodai: Interrogator-Chaplain of the Dark Angels. A major buzzkill, and batshit crazy, but more famous than his boss.
- Sapphon: High-Interrogator of the Dark Angels, at odds with Asmodai over practically everything.
- Grimaldus: Reclusiarch of the Black Templars. A seriously hardcore bastard who defended Helsreach.
- Xavier: Famous Salamanders Chaplain, meaning he's a major bro.
- Ortan Cassius: Master of Sanctity for the Ultramarines. Responsible for the formation of the Tyrannic War Veterans, to better help combat the menace that almost devoured all of Ultramar.
- Ulrik the Slayer: High Wolf Priest of the Space Wolves. A wild bastard who survived the First War of Armageddon and also has Leman Russ' own helmet. Angron himself saluted this dude's combat prowess.
- Kardan Stronos: Iron Hands Iron Father. Was elected to act as Chapter Master by the clan council. Also has a massive boner for Razorbacks, and an equally large hate-boner for the Necrons.
- Astorath the Grim: Blood Angels Master of Sanctity and Redeemer of the Lost. His job involves rounding up those in the Death Company and then lops their heads off, as they're pretty much lost causes by that point.
- Lemartes: Blood Angels Chaplain who's badass enough to rein control over the Black Rage. Keeps an eye over the Death Company as Guardian of the Lost. He is currently the second most 40K thing in 40K, being the patron saint of always being mind-shatteringly angry, closely beat out by the Eversor Assassin.
- Mikelus: Blood Ravens Reclusiarch who was said to have beaten the Necron Lord of Kronus...according to Davian Thule. Everyone else can attest to him dying like a bitch to the 'cron Lord's incredible amounts of cheese. But he was a nice honour guard member so it's okay.
- Durendin: Chaplain of the Grey Knights who appears in the first story of Justicar Alaric. Known for wielding relic nemesis force lightning claws passed down from the early days of the chapter.
- Diomedes: Former Honor Guard Captain turned Chaplain in light of his never waving faith and loyalty in the emperor when the Blood Ravens chapter master went full-heresy. His great oratory skills spur on his brothers in the battle for baldness. Believes that in a mad age, the madmen should lead the way.
- Daenyathos: The Spiritual Liege of the Soul Drinkers chapter and a traitor who used his influence and reputation to turn the Soul Drinkers away from the Emperor. His vision was to rule the galaxy through suffering and the enslavement of Chaos. He turned the Soul Drinker's entire Reclusiam into his personal agents of corruption.
For 90 pts Chaplains have a Veteran stat line with +1WS, 2Ws, and LD10. They've got a bolt pistol and Crozius which counts as a powermaul, and a 4++, with access to Terminator armor, ranged, special issue, and chapter relics like other Independent Characters. Chaplains are more a support character than a singular power house, giving their unit re-rolls to hit, and Fearless. Vanilla Marine's chaplains have no choice in melee weapons for some reason. Odd considering that codex represents the broadest spectrum of chapters. Only getting to take a powerfist, in place of their pistol.
Dark Angels have two: regular ones and Interrogators. Regular ones are identical to the above, but cannot take Terminator Armor and Chapter Relics. They do however have access to melee and ranged weapons. Interrogators come for 20 more points and get the Deathwing, Preferred Enemy (Chaos) and Fear rules and a near-captain stat line with -1WS, and access to every piece of wargear expect heavy weapons, they practically outstrip regular Captains in every way unless you pimp out a captain with loads of expensive gear. If you use them they're best used in either the Black Knights or Deathwing Knights.
Wolf Priests are probably an oddity among the Space Wolves, since they can take multiple ranged options but no melee. They also have access to Chapter Relics, Terminator Armor and Runic Armor, other than having a 4++ thanks to the wolf talisman. Having the same stat line of regular chaplains, these guys are even more support-focused than their vanilla counterparts. Thanks to the half-apothecary gig, they give Feel No Pain(6+) to the unit they're in, along with Favoured Enemy, making them the perfect scrub-sitters, making the weakest units in your army able to hold their own in a fight, especially if supported by big numbers. Wolf Priests also have Counter Attack and Acute Sense, much like every other unit in a Space Wolf army. Best use for a Wolf Priest is to stick them in a big Blood Claws unit (or even better, Swift Claws) and use them to target the opponent's infantry. Favoured Enemy allows you to use an abundance of plasma guns with relative safety and kinda makes up for the Blood Claws' WS3 and BS3, while FNP gives your guys a chance to last even against stronger opponents, at least for a while. Unfortunately, the lack of melee options means the Wolf Priest is not gonna be much useful in challenges against MEQs, so you better give him a Wolf Guard pack leader properly kitted for the task, while the Wolf Priest and the Blood Claws drown the rest of the enemy unit with the sheer amount of attacks.