I needed exactly this for my recent application, and couldn't use any application server specific techniques as I needed some console apps run on cronjobs to access them too.
I basically made a couple of small tables to create a registry-style configuration database. I have a table of keys (which all have parent-keys so they can be arranged in a tree structure) and a table of values which are attached to keys. All keys and values are named, so my access functions look like this:
openKey("/my_app");
createKey("basic_settings");
openKey("basic_settings");
createValue("log_directory","c:\logs");
getValue("/my_app/basic_settings","log_directory");
The tree structure allows you to logically separate similar data (e.g. you can have a "log_directory" value under several different keys) and avoids having the overly verbose names you find in properties files.
All the values are just strings (varchar2 in the db), so there's some overhead in converting booleans and numbers: but it's only config data, so who cares?
I also create a "settings_changed" value that has a datetime string in it: so any app can quickly tell if it needs to refresh it's configuration (you obviously need to remember to set it when you change anything though).
There may be tools out there to do this kind of thing already: but this was only a days worth of coding and works a treat. I added command line tools to edit and upload/download parts or all of the tree, then made a quick graphical editor in Java Swing.