System.Deploymentを参照して、
以下
using System;
using System.Deployment.Application;
/// <summary>
/// バージョン番号取得。ClickOnceで実行した時だけ取得される
/// </summary>
/// <returns></returns>
public static string GetClickOnceVersion()
{
if (!ApplicationDeployment.IsNetworkDeployed) return String.Empty;
var version = ApplicationDeployment.CurrentDeployment.CurrentVersion;
return string.Format("{0}.{1}.{2}.{3}", version.Major, version.Minor, version.Build, version.Revision);
}