Who installed this Emacs?
The second emacs came with OS X.  For files that are logged in the package database, you can use pkgutil:

$ pkgutil --file-info /usr/bin/emacs
volume: /
path: /usr/bin/emacs

pkgid: com.apple.pkg.BSD
pkg-version: 10.9.0.1.1.1306847324
install-time: 1382483268
uid: 0
gid: 0
mode: 555


A list of packages can be obtained via pkgutil --packages.  However, note that—again—this only covers items in the package database.

You should not modify items that are part of the core operating system.  If you prefer a locally-installed program to override one that came with the operating system, you should adjust your PATH to prefer that program before system paths such as /usr/bin are checked.

One way to do this is to have /usr/local/bin be first in your path and link your /Applications version of emacs to /usr/local/bin so that it will be called first unless a program explicitly calls /usr/bin/emacs