Even in the event they are not, I expect the only differences will be in the method of compilation (i.e. compiler used and any options set) and any extraneous packaging (such as having a bash emulating shell as in msysgit). The actual product (Git itself) should remain broadly similar.
Edit: Thanks to Jarrod for pointing this out. I've left the above in for posterity. To quote the wiki:
msysGit is the development environment
to compile Git for Windows. It is
complete, in the sense that you just
need to install msysGit, and then you
can build Git. Without installing any
3rd-party software.
msysGit is not Git for Windows; that
is an installer which installs Git --
and only Git.
It is easy to see the difference: the
installers for Git have the prefix
Git-, the msysGit installers have the
prefix msysGit-. Another telltale is
that the msysGit installers come in
two flavors: fullinstall and
netinstall. Further, msysGit does not
install to C:\Program Files by
default. But msysGit comes with gcc,
the GNU C Compiler.
"portable" version of Git for Windows (MSysGit) does not need tobe installed. It will run from any directory you place it in, evenonto a USB thumbdrive. It will not write permanent entries into the Windows registry. It does not need administrator privileges to "install". This version does not offer you the convenient right-click context menu entries "Git GUI Here" and "Git Bash Here", because these would require to add entries into the Windows registry.
The titles on the download page have just been updated so that the "Git for Windows" versions are fully identified. There is now both an 'installed' version (with right click menu options), and a Portable version that runs direct from a memory stick etc.
Git for Windows is the software package that installs a minimal environment to run Git on Windows. It comes with a Bash (a Unix-type shell), with a Perl interpreter and with the Git executable and its dependencies.
On the other hand, msysGit is the software package installing the build environment that can build Git for Windows. The easiest way is to install it via the net installer.
Git for Windows used to be developed using the development environment called "msysGit", but roughly coinciding with Git 2.1, msysGit was superseded by a new development environment: the Git for Windows SDK.
(Now) they are the same (as of May 2015 but likely a bit earlier):
"msysgit" and "Git for Windows" have merged under the name "Git for Windows." msysgit.github.io now hosts "Git for Windows" and the main git download site git-scm.com lists msysgit.github.io as the maintained build for windows.
... we decided to just phase out the name "msysGit" (as well as the GitHub org of the same name) and work on Git for Windows (with the corresponding GitHub org, and using the name "Git for Windows" for the installer aimed at "end-users" and "Git for Windows SDK" for the development environment targeting Git for Windows developers).
Git for Windows is probably what you want. It includes the following primary features:
Git BASH Git for Windows provides a BASH emulation used to run Git
from the command line. *NIX users should feel right at home, as the
BASH emulation behaves just like the "git" command in LINUX and UNIX
environments.
Git GUI As Windows users commonly expect graphical user
interfaces, Git for Windows also provides the Git GUI, a powerful
alternative to Git BASH, offering a graphical version of just about
every Git command line function, as well as comprehensive visual diff
tools.
Shell Integration Simply right-click on a folder in Windows
Explorer to access the BASH or GUI. The Git-Cheetah plugin also
provides a TortoiseSVN-like interface that displays Git functions
directly on the context menu.
The following is available as a separate download from the same page...
msysGit is a build environment that includes all the tools necessary for developers who want to contribute by writing code for Git for Windows.
Git BASH delivers a familiar environment for Linux experts who occasionally need to use a Windows machine -- even if they don't need git itself. It starts with the BASH prompt and adds a collection of core utility programs such as ssh, find, grep, vi, awk, and of course git.