I have been suffering from mainly Mail.app unable to search full-text of my emails for a couple of months. I also recently noticed that Spotlight is not searching my PDFs in my user directory. But it can find other files. I tried to fix the Mail full-text search problem numerous times, but it did not work, such as by simply reset Spotlight indexes.
Today I finally fixed it by following instructions here. Basically, you have to boot into recovery mode and open terminal, type in “resetpassword”, select your main user, and instead of changing password, select reset ACL at the bottom.
After reboot that did not immediately solve my problem. So I deleted “com.apple.spotlight*” and “com.apple.systemuiserver” from ~/Library/Preferences. Also, I tried some other commands from Terminal, which I tried before, such as hdutil -E -i off/on ~/
See detailed discussion here. Note that “on/off” above means that you turn off and then turn back on.
Anyway finally it solved my problem. I think it is a combination of a few causes. My user folder permission was definitely kind of broken. But now I am so used to Sparrow Lite email client, I am not sure whether I want to go back to Mail.app.