You should not lose anything (except access to run PowerPC applicaitons) when you perform your upgrade. As always, there is a chance that you might have probelms with the upgrade, so it is wise to make a full system backup before you start the upgrade. By doing that, if you do have issues, you will have a current backup to restore from.
There may be some applications that are incompatible which the upgrade may remove and place in a folder called "Incompatible Software" (see here: http://support.apple.com/kb/HT3258). However, beyond this it should not touch your system setup, and should definitly not remove or alter your personal documents.
However, before installing any update do be sure to fully back up your system with Time Machine so you can restore it if needed.