Oh, yes. I do Dropbox syncing, too (this is the other good thing about org-mode: plain text files). And there might be some truth in the statement that while org-mode is excellent for a single file, things start to be less seamless when it comes to more of them... inter-file links don't seem to be that reliable, for example. Is this the reason for your One Big Org File?

For white on black, it's just (setq default-frame-alist '((background-color . "black") (foreground-color . "white"))) in your .emacs.

Actually, it's kind of typical lesswrong that I started off with a comment popularizing org-mode, but ended up changing my mind about it (well... kind of), the newest experiments include Notational Velocity (they seem to be good at the global search stuff org-mode is lacking, but not so nice indented lists locally), and also this system:

http://www.speakeasy.org/~lion/nb/book.pdf

which includes paper notebooks, maps of your thoughts and similar fancy stuff, but I haven't yet finished reading it (it's long and not exactly the most organized stuff I've ever read... but it has good ideas.)