I kind of get how the indexing in Magento works, but I haven\'t seen any good documentation on this. I would kind of like to know the following.
Magento indexing is not similar to normal database indexing and is more like database denormalization (http://en.wikipedia.org/wiki/Denormalization) process. In most cases it takes the EAV structure and makes it available for flat table structure which is by no doubt faster to access and search through.
If your normal EAV query would be 200 left joins to get all the products in catalog and data over their attributes and layered navigation values then after "indexing" this data is available through denormalized data structure for faster querying/access