We almost all want clan wars, but making it happen is definitely a complicated task. I realize that this suggestion is incomplete at best, but then again, there are very few detailed suggestions on this anyway. Well, here goes:
Stage 1: Clan matchmaking/war declaration
The easiest way to do this is simply randomly match clans with each other based on their clan trophies, similar to current matchmaking. Again, this is where the importance of having players value trophy comes into play.
Now, once two clans are matched with each other, they are at war. No accepting/denying the war (there is a way out though, as explained later). Clan wars last for one week, and are only done every other week. Clan wars end one week, the league season ends the next.
Stage 2: How the wars work and Scoring
Once a war is started, there will be a new button on the attack page for "Clan Battle". This would work like normal search, essentially. It would randomnly bring up an opponent from the other clan that isn't shielded or online, and you can either attack it or return home. There will be NO skipping, and a cooldown of 30minutes (or whatever is deemed appropriate) if you decide not to attack. This way, it becomes more difficult to attack a specific target and prevents the war from becoming overly burdensome on the players (so you aren't always attacked as soon as you log off just because of the war).
The objective of the clan battles (which are normal, 1 on 1 raids) is trophies. Resources won/lost has no effect on the outcome of the clan battle. Clan battle trophies could possibly be assigned similar to normal trophies, so if you get matched with a significantly lower trophy player, you can only win a few trophies (or vice versa). In fact, I suggest that players win/lose the normal trophies as well. A defensive win adds the trophies to the score of the defender's clan (defensive losses do not affect the clan battle scores). The winner of the clan war is the clan with the most total trophies won.
Stage 3: Prizes
Clearly, the victorious clan needs to get some form of reward. I suggest that the rewards be somewhat similar to league bonuses, in that the rewards get much larger for clans with higher trophies. These rewards are the same for every member of the winning clan.
Now, what the rewards should be and how big they should be is difficult to determine. They could be either resources, a small number of gems, or perhape some special prizes (reduced training times for 4 days or 7 days of doubled collector production, for example). I'm not going to throw out any specific numbers here, though.
Special Cases:
1. What if a clan doesn't want to compete?
Maybe they have several members on vacation or maybe they just don't think they have a shot at beating the opposing clan. No problem. Have the leader of the clan have the authority to "forfeit" the war, but only during the first 24 (or 48 perhaps?) hours of the war. In this scenario, the withdrawing clan suffers no penalty, but the other clan does not receive the full reward for "winning" either. Intead, they get 1/3 of their bonus' size or duration.
2. What if members of a clan leave or are kicked?
If a member leaves, he/she can no longer attack members of the opposing clan, but any attacks (or defensive wins) that had already occured still count. However, members of the opposing clan still can attack that player and have any wins added to their score (defensive wins do not add to the player's former clan battle score). If perhaps the leader feels that the player who left could be losing purposefully, or otherwise wants the player removed from the war, he/she has the authority to remove them from a "war roster" of sorts. This roster does not change for any other reasons than the leader removing a player who has left or a player is kicked. If for any reason a player leaves and returns, it is if nothing happened. This means visiting other clans is still permissable, just you can't attack while gone.
As indicated above, if a player is kicked, he/she is removed entirely from the process. No more attacking or defending from the members of the other clan. As for the previous contributions of the player to the war, they still stand. If a player is kicked and is allowed to return to the clan, he/she does NOT reenter the war on offense. However, the player is still subject to being attacked if back in the clan. This amounts to a penalty for kicking and re-accepting, but not for any actual kickings.
3. What if new members join during the war?
Nothing. If you weren't on the war roster at the beginning of the war, you can't be added.
4. What if one clan has signficiantly more members than the other?
Even if two clans have roughly the same trophies, one could have 20 more members than the other. I recommend setting a limit to this discrepency, possibly +/- 5 members?
I'm sure there are plenty of things I didn't adress, but maybe this is a relatively simple and feasible way of making it happen? I dunno, but I tried.
This was originally posted in this thread, HERE, but I would like to hear some more feedback on my proposal.

