For iFolder 3.6 (I have not tested earlier versions) you can extract the install files with the following steps:
1) Download the client install from the iFolder server.
2) Run the installation.
3) Go through the motions of the .Net Framework installation.
4) When the "iFolder 3 Client InstallShield Wizard" window shows, use windows search (with the hidden and system folders option) to find the file "iFolder 3 Client.msi".
Copy the MSI to a known location.
Then all you need to do for your workstation installs is the following:
1) Prepare a dotnetfx (version 2.0) silent install and distribute it.
2) Use the following command line to install the iFolder client: msiexec /i "iFolder 3 Install.msi" /qb!