Many people have one or more Commander decks that they've been playing for years and still enjoy to play, but the sad fact of the matter is that even your favorite deck won't survive forever. There are a lot of reasons to set a commander aside. Maybe your playgroup is fed up with a deck and refuses to play against it; maybe a better option has been printed for the sort of game play you crave; or maybe, just maybe, the deck is no longer fun to play.
A large part of Commander's draw is the promise of unique and ever-changing game play. Run fifteen games with a Standard deck and your future games will probably start to run together, but your fortieth game with a Commander deck is still full of new interactions and discoveries. At least, that's the theory.
The more tutors you run, the more quickly games go stale. The more cards that serve similar roles you pack into your deck, the more quickly it stops feeling fresh. The more heavily you build your deck around your commander, the more quickly you get bored. You can go tutorless, you can avoid doubling up on effects, but at its core, the format discourages disregarding your commander. Increasing your deck's lifespan is a great thing, but it's not worth abandoning the format for. I, for one, would rather play a Commander deck for a few months than a normal Highlander deck for years.
Then again, we have a tool to combat repetitive game play beyond the actual deck list: building more decks. This solution isn't always feasible; those of us with limited Magic budgets can't just amass more and more Commander decks without ever trading away the old for the new, but if a deck has been your favorite for years and is just now getting boring, you might consider setting it aside for a couple of months rather than tearing it apart. Repetition is unpalatable when it's fresh, but playing a familiar game after a long break will be nostalgic rather than grating.
Don't you miss Winter Orb?
On the other hand, not all fun can be preserved. Some decks are fun because they let you do something genuinely enjoyable, such as attacking with creatures. Others can be fun for a while, but will have a hard time fulfilling their quota of enjoyment down the road. Some decks are fun because they're novel.
When Double-Faced Cards were first announced during the Innistrad spoiler season I was unimpressed. The cards seemed to be causing a lot of logistical problems without much gain. But once I held one in my hand I was convinced otherwise. As some one who has played this game for a decade, I have a strong mental image of a card; at the moment flipping over a DFC when I catch the first glimpse of an unfamiliar back, I'm always surprised. Playing with DFCs feels like I'm breaking an ancient covenant; it's invigorating and frightening. Not so for new players. Without a long association between the fronts and backs of Magic cards DFCs aren't so strange, and thus lose much of their appeal. In time the same will happen to me; I'll get used to them and they will no longer be exciting. Double-Faced Cards are an extreme example, but playing Dredge or Storm is very much the same; once you grow bored of playing Jhoira of the Ghitu, you'll never be able to recapture the initial rush of excitement you felt suspending Darksteel Colossus. If you're bored with a deck, you need to take a good, hard look at what made that deck fun to play so that you can determine whether or not simply giving it a rest will be enough to rekindle the flame.
Of course, not every deck you come up with becomes an instant favorite. When you have a flash of inspiration, you might as well give it a try. Sometimes things work out and you end up with a new favorite deck, but the majority of the time your brand new deck won't succeed at being everything you hoped it would be. The question is whether it failed in concept or execution.
Being not only a casual format, but a very slow one, Commander allows for a near infinitude of viable game plans. Pretty much anything that's fun can be made to work, so if your new deck isn't playing out the way you want it to, but the initial idea still seems worthwhile, don't give up! It may take quite a bit of tweaking, or even overhauling the entire deck list, but there's almost certainly some way to make your idea work. The experiment isn't a failure because your first iteration didn't live up to expectations, that's just your first data point among numerous potential builds. Failure only occurs when your deck-building is a success. Let's take a recent example.
When the Magic: The Gathering Commander decks were revealed, I was ecstatic at the prospect of putting Riku, of Two Reflections to work leading a Warp World based Commander deck. I love huge effects and getting value out of enters the battlefield triggers, and I'd wanted to build a Warp World deck for a long time. Riku promised adequate ramp, token production, and tutoring to make World Warping a viable strategy, and copied the deck's namesake sorcery on top of it. What could go wrong?
Did the deck play out wrong? Was I unable to find Warp World? Or not getting value out of it? No. Everything came together perfectly; the problem was that the idea didn't have to potential to be fun. Warp World is great when it's a big shift from the norm, but as soon as it starts going off every game, or multiple times per game, it stops having the same effect. The first problem is in resolving Warp World itself; doing so requires a lot of counting, shuffling, and stacking triggers, all of which feels futile when another copy is sitting on the stack ready to undo all of the work you put into figuring out the new board state. On top of that, once the spell becomes commonplace, people notice that it doesn't do what it promises to. Warp World says it's going to make a chaotic board state in which power is redistributed arbitrarily without starting the game over. In actuality, it puts its caster, who has undoubtedly built around it, way ahead while mana screwing all of the rest of the players and stopping their game plans cold. Playing a couple of games against Warp World shatters the illusion and robs the spell of its appeal.
If your experiment fails like this, it's best just to scrap the idea entirely. Sure, you might be able to tone the deck down to a point where people are willing to play with you, but unless it's absolutely the most fun you've ever had playing Magic, you'll be better off playing something everyone can get behind. It can be painful to admit a concept that you've put a lot of work into simply isn't going to work out, but this momentary strife is well worthwhile if it means you can go back to having fun playing Commander.
Cold Hard Facts
Up to this point we've been floating in the wonderland of Commander theory, but sometimes reality has other thoughts. Building decks is expensive. Sure, shelling out $100 for a new Commander deck might not be as bad as building a new Legacy deck from scratch, but it's not exactly cheap either. To ease the strain on our wallets, most of us trade cards we're not using for whatever it is we're looking for. It's just impractical to keep a deck together if you don't play it; those cards could serve you a lot better trading for something you'll use, but sometimes the cards you don't use aren't enough, and you'll have to take apart a Commander deck you do play in order to build a new one. I've certainly taken apart my share of decks that I still played occasionally to avoid having to acquire yet another set of Demonic Tutor, Vampiric Tutor, and Sol Ring. Then again, I usually have a deck sitting around that should have come apart a long time ago anyway.
Turning it Over
Take a look at your decks. Are you clinging onto one that just isn't fun to play anymore? Would you be better served by trading one's parts to build the deck you've been yearning for? Scrapping a deck you've poured your time into certainly isn't fun, but often it is right. It's easy to espouse ideals, but harder to act on them. I should probably take apart my Shirei, Shizo's Caretaker deck: it's not a whole lot of fun for the other players at the table, and it's losing the novelty that endlessly recurring creatures brought. I've foiled out almost half the deck, and more than that, Shirei was the first commander I really enjoyed playing. I haven't worked up to setting it aside yet, but at least this way I can be held accountable. Good luck in your own battles!