Assassin's Creed has the Arc Words of "Nothing is true, everything is permitted" and examines how this idea evolves and applies to different individuals and contexts.
The real theme is the struggles of history itself, that our ancestors are humans, and for all our relative progress, people are still the same more or less. Great figures in history have Feet of Clay and are more human and down to earth than expected and that humanity is only the inheritance of all past achievements and that descendants have a responsibility to make "all this suffering worth something".
The struggle between the Assassins and Templars is about the nature of power and freedom. To what extent do people need leaders to define and direct their lives and to what extent does democracy work, both the Assassins and Templars have a millennia long philosophical debate over this with no real resolution, with the running theme of compromise, failure and Humans Are Flawed.
The theme of the second game is specifically a question of whether criminals deserve basic fundamental human rights, to what extent do the worst of humanity command compassion and restraint and what does it say about a society that decides to wash their hands off them and simply corral them to a dustbin where they will eventually be subject to Kill 'em All.
Via Word of God, the series' other central theme is that you need to let go of the past. In New Vegas in particular there is a direct correlation between a faction's evilness on the karma meter and how tightly they cling to the values of the past.
Fallout: New Vegas has a theme beyond that, and a different one for each DLC. In the game overall, it's that all power is a gamble (appropriate for Vegas) and small things can tip huge scales.
In Honest Hearts: We're all tribes in the end and family forgives no matter what, so long as you admit that you went wrong.
In Old World Blues: The Wasteland may be harsh, but the Old World was no kinder. Look to the future - not for something better, but to make it better.
In Lonesome Road: One person with one careless action can leave unimaginable scars, and the power of symbols - particularly flags.
The theme of letting go of the past plays a key role in each DLC. In Dead Money, the fall of the Sierra Madre came from its owner's efforts to keep the woman he loved safe forever, and the main plot is driven by each character's inability to let go of the reasons why they originally came to the Sierra Madre. In Honest Hearts, you decide whether Joshua Graham lets go of his past or embraces it. In Old World Blues, the peaceful ending of the DLC has you convincing the Think Tank they need to let go of their mad science and leave the Mojave be. Finally, Lonesome Road centers around Ulysees' inability to let go of the ideals of Hopeville after the Courier unknowingly caused its destruction.
It's said war - war never changes. Men do, through the roads they walk.
Far Cry 2: War for the sake of war, and that eventually the only way to make it end is to save the innocent and kill everyone else, including yourself.
Far Cry 3: Insanity, the blurred line between fantasy and reality, and whether or not a normal person can ever be good again if they choose to go down the rabbit hole and embrace their inner warrior.
Killer7: Every nation has its own culture, and one nation forcing its culture onto another will only make the other nation bitter.
Kingdom Hearts: Chain of Memories: The nature of memory seems to be observed in this game. All kinds of memories are observed, from Sora's true memories to the fake memories of the Riku Replica. The game even seems to suggest that even false memories can be of importance.
Heck, the entire series has a good basis on analyzing memory, not to mention friendship.
The Last of Us: Partnership. Just about every named character has or had some sort of partner or companion.
Selfishness comes in at a close second. There's rare exceptions but the motivations of almost all the characters have some degree of selfishness to them.
Left 4 Dead is interesting in that the theme - The Power of Friendship - is almost entirely told through gameplay, e.g. committing traitorous acts such as running away from your team will draw a tank or hunter to you, getting you and probably everybody else killed.
The developers of the first game in the series described its core motif as "What is evil? Perhaps it is only a perspective." This theme has coloured every game in the series to a greater or lesser extent, with its extensive use of Grey and Grey Morality.
Legend Of Heroes VI: No one person, no matter what they've done in the past, no matter what they've done with their lives, is completely beyond love and redemption. Any life can be given meaning so long as you're willing to reach out to a person.
MadWorld: Humans Are Bastards, and this isn't about to change any time soon. All you can really do is is stiffen your spine and keep going.
Mass Effect: Can a single person change the fate of the galaxy?
Also the fact that sometimes, no matter how hard you try or how well you think you're doing, you can never get a flawless victory. Sacrifices must be made, and you can't save everyone. Despite this, things can always get better.
And actions that you take, no matter how small or insignificant, can come back to haunt (or help) you later. We are the summation of our choices.
Centrally, the story of all three games seems to have a great deal to do with the emergence of AI and the way the inevitable conflict with organics will be played out or resolved. This itself can be tied into the greater theme of parenthood and creators-verus-creations. We dare you to find a single main character in the game who doesn't have some sort of family issue. If you actually do, they'll probably instead have issues with their mentors, trainers, employees/employers, oldest friends, or someone else who could be said to have created or been created by them.
The risks of cultures and societies achieving things they haven't earned are presented multiple times throughout the series, and are central to the choices at the end of all three games.
No matter how impossible it may seem, a Third Option can be there when you need it most.
Your past will haunt you for the rest of your life.
On another note, the games also have themes that are often summed up in a single word. The first Metal Gear Solid had the theme of "GENE". The theme of MGS2 was "MEME". The theme of MGS3 was "SCENE". The theme of MGS4 was "SENSE". The theme of Peace Walker was "PEACE". And the theme of Revengeance is "REVENGE". For Metal Gear Solid V, the themes are pain and loss. Or, more accurately, the pain that comes from a loss. These themes tend to crop up a lot in the game that they describe, although they are often referenced in other games. To the extent that mission packs for the multiplayer of 4 were named the "GENE" "MEME" and "SCENE" expansions, and all included elements from MGS1, MGS2, and MGS3 respectively.
Most themes in the game (including whether it errs on the side of Screw Destiny or You Can't Fight Fate) depends on how you play it and personal interpretation of the ending. However, one of the larger ones, one that links in with the Arc Words ("What can change the nature of a man?") is that of Change. What changes, what doesn't, and whether anything can't.
The Reconstruction: Scope; the necessity to understand all sides of the story and the full truth before one can make the correct decision, and the danger of jumping to conclusions. However, you must acquire the necessary knowledge without also losing sight of what is truly important.
"How far back must we stand before we can see everything ahead? And...does that mean we must lose sight of what was closest to begin with?"
I Miss the Sunrise is the inverse of this; whereas The Reconstruction's scope went from small to big, here the focus is on big to small.
Rise of Legends: In the end, is there any difference between magic and technology?
Quite unusually for an over-the-top, uber-silly action game, Sengoku Basara 3 has a fairly downbeat one, seeming to be about how all the fun times and glory days are either over and done with or coming to an end. Instances include Mitsunari's total anguish over the death of Toyotomi Hideyoshi, Motochika constantly muttering "those days are long gone", Oichi degenerating into a Psychopathic Woman Child, Yoshihiro still fighting despite knowing his generation's practically over, the lack of well-known characters from previous games due to plot purposes... oh, and being set at the very tail-end of the Sengoku Jidai is a fair indicator. Still, considering the plotline about Tenkai attempting to resurrect Demon King Nobunagaand succeeding, maybe it is telling us that it's better to move on.
Rule of Rose: The difference between an adult and a child's mentality, the difference between fairy tales and reality (and how the two combine), and the different forms of love.
Sonic the Hedgehog CD - Technology is not inherently evil as long as mankind does not misuse it. The Bad Future shows us a portrait of a world overrun completely by technology but Good Futures illustrate technology and nature co-existing in harmony, making for a better Little Planet.
A common motif in this game seems to be misunderstanding. For example, Sonic is mistaken for Shadow and wrongly arrested. Shadow misunderstands Maria's final request and nearly destroys humanity instead of protecting it as she wanted him to.
Sonic the Hedgehog (2006) - A question often asked in this game is whether or not one person should suffer for the good of the world. Since Elise is used as a living seal for Iblis the world is safe from destruction, but she obviously suffers from it and has to force herself not to cry so as to not release the god through her tears. After being confronted about it by Amy, Silver wonders whether or not it's right to kill Sonic to save the future and later on in the story Silver is reluctant to seal Iblis inside of Blaze thus sending her into another dimension and out of his life even though doing so will keep the world safe. At the end of the game, when Elise has to blow out the Iblis Flame to stop it from ever existing, she is hesitant to do so since that will erase the meeting between her and Sonic. She even cries, "I don't care what happens to the world!" She has to choose between herself and everyone else.
Super Paper Mario - The Power of Love, any and all love. All the bosses represent some form of perverted love, and all the characters showing genuine love end up redeemed. Almost every NPC talks about or shows some form of love, whether it be romantic love, friendship, familial, even love for the environment.
Tales of Symphonia: It's never too late to atone for one's sins. Every life has value, and everyone deserves the right to live happily.
Tales of Vesperia: Making your own choices. It's better to choose what you want to do or what you feel is right, rather than resign yourself to what others expect of you or what you think you have to do.
Tales of Xillia: It is better to work together to forge a better future for everyone instead of mindlessly devoting yourself to a single cause.