I've just finished the folder tree panel for BH/e, and because I'm a kind, caring developer (ahem), you get some pictures...
It's your basic AJAXy tree system, where you click on a folder's > picture, a little loading spinner appears, and then shortly afterwards the subdirectories appear below. Currently it reloads every time you collapse and re-expand a folder; I'll be working on making that more efficient later.
I've been debating about where to put the folder tree view and if I should integrate it with the main file view and have everything all in one. I think it's best to have it as a sidebar, both because people are used to that, and because it means having a lot of files in a directory doesn't push the next lot of folders off the bottom of the screen.
I might stick a breadcrumb bar in above the file list, though.