Where do you put your resource files?

[eluser]Basketcasesoftware[/eluser]
I've been putting my resources folder in the same location as my system, index.php, and application folders. I try to hide my application and system paths as much as possible and I feel that the tendency to need to put full path names for certain objects will reveal the existence of my app and system folders if I put the resources there. But I've seen other people suggest putting resources in you application folder. Where do you put yours, and why?