Quicksilver and Spotlight
Alfred uses the Spotlight index by default, and LaunchBar also has an option to use it. The Spotlight index includes almost all files, so you don't have to adjust what files to index manually.

By default, Alfred is conservative in what types of files it searches for, to avoid muddying your search results. You can tick the boxes for what parts you want to be included in the results by default. If you want to search among all files on the system, you just need to press the spacebar before you begin typing the search term, and it will then search the full Spotlight index rather than just a subsection of it. You also have the open/find keywords, which likewise search the full Spotlight index.

If you always want it to search the full index, then you can enable that option in the preferences. Despite the warning, Alfred is pretty usable (and very fast) even if you enable searching for all files.



(It still excludes the system files that are hidden from normal Spotlight results. But you can search for those by creating a search filter.)