Magento – completely disable an indexer

You could just touch the lock file.

<?php touch('BP.DS.'var'.DS.'locks'.DS.'index_process_1.lock')

or

#!/bin/bash
touch /home/path/public_html/var/locks/index_process_1.lock

This is obviously a low quality solution - but if you wanted to perform this action peripherally to Magento (eg. from a bash script, it would be suitable).

Otherwise, the methods you need are in Mage_Index_Model_Process

Such as isLocked(), lockAndBlock(), and unlock()

Assuming your module extends said class, you need only declare

const PROCESS_ID = 'my_indexer'

And use the methods as appropriate

$this->lockAndBlock();

In order to declare an index you need to add this to config.xml inside the global tag:

    <index>
        <indexer>
            <some_unique_index_name_here>
                <model>[module]/indexer_something</model>
            </some_unique_index_name_here>
        </indexer>
    </index>

The model tag in the code above contains the alias for your indexer model. It's similar to the one you use for Mage::getModel(...).

Then you need to create the class referenced in the model tag above:

//you need to extend Mage_Index_Model_Indexer_Abstract class
class [Namespace]_[Module]_Model_Indexer_Something extends Mage_Index_Model_Indexer_Abstract 
{
    //you need to add the following 2 methods `_registerEvent` and `_processEvent`. Let''s just make them do nothing for now.
    protected function _registerEvent(Mage_Index_Model_Event $event) 
    {
        return $this;
    }
    protected function _processEvent(Mage_Index_Model_Event $event) 
    {
        return $this;
    }
    //this is the index name that shows up in indexes section
    public function getName() 
    {
        return Mage::helper('[module]')->__('Your index name');
    }
    //this is the index description that shows up in indexes section
    public function getDescription() 
    {
        return Mage::helper('[module]')->__('Your index description');
    }
    //magic happens here
    public function reindexAll() 
    {
        //here goes the code you need for reindexing
        return $this;
    }
}

If your index needs to run only from the indexes screen or command line then you are set.
If you need your index to be triggered at different events it gets more complicated.
You need to implement the methods that I left blank above _registerEvent and _processEvent.
But these are really specific depending on your events.
You can take a look at these methods from the core indexers to see what happens.
The flat product indexer for example: https://github.com/OpenMage/magento-mirror/blob/magento-1.9/app/code/core/Mage/Catalog/Model/Product/Indexer/Flat.php