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Castle: In the ongoing story-arc, what cost seeking justice for the wrongs of the past can have on the present and / or future. In general, the perils and opportunities of opening yourself and your heart up to someone else.
Cheers: Everyone needs to have somewhere to come home to.
The series as a whole focuses on how people bond together to form communities with one another, and what it takes to hold these communities together; in particular, how friendship and accepting others, flaws and all, helps with this. Each season also develops a particular aspect of this theme, based around the class that the main characters are taking together for that year:
Season 1 (Spanish) - Communication; how do people of different backgrounds learn to speak a common language with one another?
Season 2 (Anthropology) - Unity; can people of different persuasions come together as True Companions? And can they stay True Companions without either tearing themselves apart or letting outsiders do so?
Season 3 (Biology) - Evolution; can the group stay together even as they evolve differently as people?
Season 4 (History) - History; the group coming to terms with their pasts but also realizing how much they've grown.
Season 5 - Renewal/Restoration and starting over; the show doesn't follow the characters as they study a particular class but as they try to make the school a better place, and thus try to figure out how start their lives over again after things have fallen apart for them. Later episodes dealt with conflict and how it is both avoided but at the same time needed to advance a story.
Overall could be said to focus on pacifism (whethertechnical or otherwise), the question of where "home" really lies and the ever-changing nature of reality. But breaking it up for each Doctor (mainly taken from the Doctor Who Ratings Guide):
First Doctor Era: The meeting of the primitive and the advanced.
Second Doctor Era: The dangers of technology. Also, the enemies outside and inside (this is the era where the 'base under siege' plot was most commonly used as a staple).
Third Doctor Era: Authority.
Fourth Doctor Era: Survival at all costs, climaxing with Season 18's message of 'change and decay' (Season 12 in contrast had an underlying theme of 'rebirth').
Early Fifth Doctor Era: "We're all in the same tribe!".
Nine's era also has "everyone can save the day." A majority of the episodes resolve themselves due to the Doctor's inspiring miscellaneous characters to be heroes.
Tenth Doctor Era: Life after the funeral. Also, the pain of immortality, and the delicate balance between being a hero and assuming that you are the only person left with the power to save people.
Arrogance and hubris, and the consequences of this, is also something of a theme. It's notable that whenever the Tenth Doctor lets his more arrogant tendencies get away from him, the consequences usually come back to bite him.
Eleventh Doctor Era: Fairytales and stories, along with "Time can be rewritten". And now in series 6, Becoming a legend will make you The Hero to some and The Dreaded to others, no matter how neutral your intentions.
Also, anyone, even the most seemingly insignificant person, is important and matters even if that person can't see it themselves.
What does it mean to be "The Doctor"?
The series as a whole has "the triumph of intellect and romance over brute force and cynicism".
Dollhouse: What is the human identity? Is it tangible? Can it be destroyed?
Faith in all its permutations. The terrible and glorious things faith can motivate people to do, how they react when their faith is taken from them, and the forms that faith comes in (religion, family, heroes, causes, love, friends, and so on). Faith itself can be more worthy than whatever symbol it's placed in.
The film Serenity, though touching on that theme in the Operative and Mal's character arc, has a different one that may have surfaced if the series had continued, which is this: Flawed humans can't create perfect humans or a perfect world. The death of what is considered 'sin' would be the end of the human race; without evil, without wrong, without the ability to choose to be good (rather than being good because that's all we can be), we may as well be dead.
Foyle's War: The moral and ethical price of fighting a war on the people living in the home front. Can even murder be considered a crime when thousands more are dying through warfare every day?
Friends: Friendship in all its forms (friendship among men and women, friendship that is broken and reforged, friendship that blossoms into romance).
Popularity is a fleeting and unsatisfactory thing, and the more you try to achieve it the more you'll hurt yourself and others.
Another theme that is brought up a lot on the show is that we all have something "wrong" with us, or something which makes us different or "freaks", but we should embrace that, take pride in our flaws, and turn our weaknesses into strengths.
The Good Guys: Crimes can't be solved without getting one's hands dirty.
Being a franchise where each Season usually operates under its own continuity, the Central Theme tends to change from series to series.
Showa-era Riders: There are a few exceptions, or at least, seasons where it is not as large an issue, but the basic unifying theme of the pre-Kuuga era is "Does becoming a monster mean losing your humanity".
This theme is still in effect in a number of the Heisei seasons given that many of the protagonists are related to or have powers related to the antagonists in some way, and in fact, some protagonists either toe the line in becoming or are revealed to be monsters and the overall conflict of humanity vs. monstrosity is reflected upon.
Kamen Rider Kuuga: If violence is needed to combat violence, then when and how does it stop?
Kamen Rider Gaim: What do I do with this newly obtained power? What do I destroy then if I don't want to destroy anything?
The Larry Sanders Show: The contrast between the slick surface glamour of showbusiness and the backstabbing grubbiness behind the scenes. Word of God also indicates that the show is about love — specifically, the kind of love between lifelong friends who care deeply for each other but struggle to express it.
Law & Order: The strengths and flaws of the criminal justice system, and the difficulties in trying to find true justice while operating within it.
Life: The difference between forgiveness and revenge.
LOST: Science vs. faith, and which one we choose to believe in during critical situations.
Mad Men: The contradictory roles men and women are supposed to play in society.
TheOffice (Both UK and US): The demoralising and crushing tedium of white-collar work.
Also, the debate on whether one should escape from the toil of this work to follow one's dreams (risking failure in the process) or to stick with it (enduring a lifestyle of monotonous labor that nonetheless grants financial stability).
One Tree Hill: The struggle of children to try to be better than their parents.
Oz: Does man have the capacity to change his wicked ways?
Parks and Recreation: Has the same theme as Yes Minister and The West Wing, but takes place on a smaller scale (city government rather than national government). It takes the idealistic approach for the most part.
Peep Show: The differences and conflicts between the appearances we present to the world and our secret inner thoughts.
Person of Interest: Who do you save and who do you kill? Do you even have the right to make that decision?
The BBC's version: For the first two seasons: what's more important, the needs of the individual or the impersonal greater good?
For the third season: fight the good fight, even if (or when) it costs you everything you hold dear.
The relationship between an individual man, the people in his life, and the legend that builds up around him (as epitomized in the gang's Catch Phrase: "We are Robin Hood".) With that in mind...no matter who dies, legends will live on, and ensure that there will always be people willing to fight against The Man.
Scrubs: When the power to save or destroy people's lives rests in your hands every day, you need your friends to help you handle the responsibility, because you can't do it all on your own. After all, you're noSuperman.
Seinfeld: How some people just will never learn a lesson, if there's even a lesson to learn.
Spaced: What it means to be a young adult in the early twenty-first century, and how that means figuring out who you are and what you want to do.
Star Trek: The possibility of friendship among races. As ugly and violent as human history has been, it is possible for us to achieve world peace and equality.
Star Trek: Deep Space Nine: Whether it is possible to break free of the past, or whether people/civilizations will be forever chained by it, at least early on. Later seasons address the Godzilla Threshold, and whether it is possible to hold onto morality in the face of certain doom.