Good questions Pieter. This is IMHO a problem if someone produces a game and add various additions over time to it. The rules seem to "hung themselves up". While there is in my knowledge no rules compilation that answers all your questions I try to answer them based on my knowledge of the game. I really like the game and play it with various additions (even added a second Starter (Carcassonne) to it so that I have enough tiles for my big table).


I am well aware that some might disagree with my answers (and having good reasons for it) but here is the way we play it:
1.Can the dragon eat a Meeple from the tower?
See my earlier posting above. For more strategy: Yes, let him eat the meeple and therefore open the tower again. No if you want to avoid the "let the dragon eat the meeple and I catch his farmer before he can react". IMHO is based on the level of "competition" you like to have in the game. The fairy will become a stratetic goal in the game, sometimes be the only way to protect your valuable farmer / city etc.
Due to the rules: A meeple on a Tower can NOT come back to his owner, so the dragon can't eat it (otherwise it would come back).
2.If there are 2 meeple on 1 tile (tower and city) does the dragon eat them both?
This problem might arise even without the Tower. F. ex. a monastery in a city. Our play is (even this situation never happened due to the fact, that both players try to "protect" the tile in moving the dragon in other directions) that the dragon then really has a feast (eating both meeples). This avoids the "whom do you like more... eat his meeple not mine".
3.Can the builder, the pig and the big meeple also been taken captured by using the tower?
A rules lawyer might say: "It says: Meeple captured..." Therefore it makes more sense in capturing the farmer (and leaving the pig alone or the builder) then capturing the pig. If you play with the Dragon expansion you still have the possibility to bring back one of your Meeples to the farm / city. Therefore try to get the meeple and see to it, that the other player never brings a meeple back. The Big Meeple is a meeple that scores double - so nothing special - capture it as a normal meeple.
This will even force the other player (because he hopes that he can bring back a farmer) to close the tower in adding one of his meeples therefore reducing his Meeple - pool.
4.If they can be captured, do you need to exchange against an pig, … of the opponents colour?
Due to the fact that the rules say: "Meeple capture", I would not allow to capture a pig or a builder.
5.If they can be captured, what do they cost to get them back?
No pig, no builder. Big meeple with big meeple OR meeple + 3 VP or 6 VP.
6.If a farmer get captured, what happens with the pig?
Leave it where it is and hope that you can bring your farmer back (possible with the Dragon expansion).
7.If a meeple from a city/road get captured, what happens with the Builder?
Leave him where he is and hope that you can bring your Meeple back (possible with the Dragon expansion).
As I said, this is the way we play it and I think it is as close to the rules as you can get, adding to the complexity of the various expansions. If I play with newbies I might even agree before what to do if one of the situations you describe arises.
It is a bit "house - ruling" but unless the "Lord of Rules" will create an official 4th edition of the rules I can live with it quite easily.
By the way: Add the Count to it and it will increase your problems, not decrease it.
Hope this helps.
The Alphawolf