For the latest version, Juniper made it pretty easy to set up a PreConfig file to use with deployment.  The web-based config can be found under the Admin portal on your VPN Appliance.  The CommandLine I used for the installation was:

msiexec /i "j-pulse-win-3.1r2-b29447-64bitinstaller.msi" CONFIGFILE="AGENCY.jnprpreconfig" /passive /norestart /q

The config file looks like this:

schema version {
    version: "1"
}

machine settings {
    version: "9"
    guid: "c7ac474e-f7f8-437c-927d-dec7a779874f"
    connection-source: "preconfig"
    server-id: "328ccbfd-c785-4208-94ed-7ecb5f8dcd85"
    allow-save: "false"
    user-connection: "true"
    splashscreen-display: "false"
    dynamic-trust: "true"
    dynamic-connection: "true"
    wireless-suppression: "false"
}

ive "a73a4fb0-f302-43ed-9655-b0b5d2504bc9" {
    friendly-name: "VPN"
    version: "2"
    guid: "a73a4fb0-f302-43ed-9655-b0b5d2504bc9"
    server-id: "328ccbfd-c785-4208-94ed-7ecb5f8dcd85"
    connection-source: "preconfig"
    uri: "VPNSERVERADDRESS"
    connection-policy-override: "false"
    use-for-secure-meetings: "false"
    use-for-connect: "true"
    connection-identity: "user"
    connection-policy: "manual"
}

Lines that might be of interest to you:

friendly-name - This is the name displayed on the connection list

uri -The address of your VPN server

connection-policy - "automatic" or "manual".  Auto will attempt to connect as soon as Pulse starts up.

take note of the remark on the installation instructions page from Juniper which states

For a Windows installation (.msi) that uses an automated distribution mechanism and where the users do not have administrator privileges, you should ensure that the installation is run in the proper context, typically the USER context. To install in USER context, first advertise the .msi while in the SYSTEM context. For example, to advertise the 64-bit Windows installation to all users, use the following msiexec command:
msiexec /jm \JunosPulse.x64.msi

(http://www.juniper.net/techpubs/en_US/junos-pulse4.0/topics/concepts/a-c-c-installing-preconfigured-pulse2.html)