I am trying to set up a Bukkit server. Is it possible to have different plugins in different worlds? I am ok with Permssions, and also I have already downloaded PermissionsEx. Could you give an example how to do it?
I'm not sure that you understand what you are trying to attempt. If you set up a minecraft server using bukkit, then you will always be loading the same world, unless you manually change what world is going to be loaded in the configurations, and even if you did, it would still load the same plugins folder as it is in a set place.
Sure, you can copy and paste the whole bukkit+server+properties+plugins and use a different folder for different worlds+plugins+properties, which would allow you to have separate plugins, but for what you are asking, there really isn't a simple point and click method for separate worlds having separate plugins.
If you want it to load a different world with its own plugins, just make a shortcut to the bukkit initializations in each of the folders you create, so its easy to choose which to start.
There is a plugin available that you can use for this called per world plugins. http://dev.bukkit.org/bukkit-plugins/perworldplugins/
Note: Perworldplugins is not up to date for 1.7.2 as of this posting.
On another note however, MOST plugins come with the configurations of "enabled-in-world". This alone should suffice enough in most situations, simply enable or disable plugins based on the world that they are in.
Although you can't have true per-world plugins, most permission plugins come with per world permissions, so only give certain permissions for the worlds you want the plugins in.
For example. I have a plugin called colourfireworks that I only want enabled in the world "firework". I would then only give users permissions in the "firework" permission file rather than the global one.
We'll I don't know any plugin but it's possible if every time you make a portal it creates a different world so if you can find that file and only give it permissions for certain world that might work and I have tried other plugins before and it does the same thing just only limit permissions in certain places