The indexing service is responsible for two things really: Making search boxes run super quickly (like under the control panel, and your program files) which is a blessing, as it does run very fast. It is also responsible for doing the same thing over all your files that you choose to let it index. This can be good if you do a lot of searches, or bad if you have a lot of files in these areas, but don't ever search them. Or even if you do search them, it can cause your indexing service to cause a lot of strain on your hard drive (or at least slow you down as it is hard drive intensive). I personnaly would not turn *off* Indexing services, but I would recommend disabling for everything else but the start menu/control panel, etc.
You can change the indexing locations:
* Open Control panel and type in 'indexing' into the serach box (or you can do this from your start menu, but many people turn it off).
* Select 'Indexing Options'
* Select Modify Button
* Expand the trees, and uncheck any areas you do not want indexed. It is a pain, as you get no indication which trees have subtrees checked, but the best place to start is Users/*your user name*/ and Users/Public.