I just discovered today why I am often taken aback by search results when using the Finder to search through my home directory. I use FileVault for protecting the contents of my home directory, which is what is causing the problems. In a Finder window, click on your Home directory, then start typing in the search field for a file or text string you know is somewhere in your Home. Make sure that Home is selected as your search target. On my machine, the results I get are identical to what I get from searching with Computer as target, and the reason is FileVault.
A way to get around this is to use the Others function to create another target container. Drag in your FileVault directory, and also add at least one other location as well -- for some reason, this does not work if you use only the FileVault-enabled home directory. Note that you can create or select a dummy folder created somewhere to get around this problem.
If you really only want to search your Home directory, you can try this rather clumsy workaround:
Mac OS X Hints
http://hints.macworld.com/article.php?story=20060601024845488