My .emacs is only 127 lines, here are the most useful little snippets:
;; keep backup files neatly out of the way in .~/
(setq backup-directory-alist '(("." . ".~")))
This makes the *~ files which I find clutter up the directory go into a special directory, in this case .~
;; uniquify changes conflicting buffer names from file<2> etc
(require 'uniquify)
(setq uniquify-buffer-name-style 'reverse)
(setq uniquify-separator "/")
(setq uniquify-after-kill-buffer-p t) ; rename after killing uniquified
(setq uniquify-ignore-buffers-re "^\\*") ; don't muck with special buffers
This sets up uniquify which changes those ugly file<2> etc. buffer names you get when multiple files have the same name into a much neater unambiguous name using as much of the whole path of the file as it has to.
That's about it... the rest is pretty standard stuff that I'm sure everyone knows about.