We have a similar issue here in my office. Currently we are migrating
from VFP to C# and reconsidering the entire opperation of our
application update procedures.

Currently we have our upgrade directory for each application, when we
make are nightly builds we place the new binary in the upgrade folder.
At midnight (all users are off the system by around 5:30-6pm) we have a
scheduled task that copies our applications to the branch offices.
These applications are simply accesses by Shortcuts on the client
machines. Each morning when they run their shortcut, it runs the newest
deployed build.

However, now that we are working in .Net (C#) we are looking at
implementing a wrapper application, or a launcher app. This application
checks their local application version against our build version data
and decides if the user needs to upgrade. At the point of them needing
an upgrade it informs them that the current application is out of date
and a new version is available.

We present them with a form that begins the download of the newest
binaries (executable and libraries) once this is completed the
application restarts and verifies that it is using the most recent
version, then allows the system to start.

Using the new method allows us to make critical changes durring the day
without the fuss of making sure everyone is off of the system. It will
simply notify them that a new version exists and they should complete
and transactions, save their data and restart their application (or
click an update button).

This may, or may not, be a valid solution for you, but in our
environment it is one that provides us with the most flexability and
consistancy.