Please ensure following checklist when deploying WebSite/WebApp which employs Intersoft controls:

1. RuntimeLicenseKey
   This is a key required in order to license the components for deployment purpose in production environment. This one is checked/done based on your post on August 13, 2015 (...excluding the Runtime Licens sections of course)
2. Resource Assembly
   Ensure that you have copied the resources assemblies to your project's bin folder. Example: ISNet.WebUI.WebGrid.Resources.dll; ISNet.WebUI.WebDesktop.Resources.dll.
3. Framework Assembly
   You are required to copy framework assemblies to your project's bin folder. The framework assemblies are: ISNet.dll; ISNet.WebUI.dll; and ISNet.WebUI.Resources.dll.
4. Component Assembly
   Component assembly is required to be copied to your project's bin folder. The component assemblies are: ISNet.WebUI.WebGrid.dll; ISNet.WebUI.WebDesktop.dll; ISNet.WebUI.WebCombo.dll, etc.
5. Feature-specific Assembly
   Exporting, charting feature assembly is required to be copied to your project's bin folder if the WebApplication utilizes these features.
6. Ensure that handlers have been added in <system.webServer> in web.config file.
   For more detail, please check this tutorial article that provides a step-by-step instruction on how to configure Web Site to run in IIS7 (or newer) environment.

I haven't tested following solution further, but you can give it a try. It adds an AutoIncrement column to the DataTable.

Snippet code of OnInitializeDataSource event handler:

protected void WebGrid1_InitializeDataSource(object sender, ISNet.WebUI.WebGrid.DataSourceEventArgs e)
{
    OleDbCommand selectCommand = new OleDbCommand();
    selectCommand.Connection = con;
    selectCommand.CommandText = "SELECT * FROM Customers";

    OleDbDataAdapter da = new OleDbDataAdapter();
    da.SelectCommand = selectCommand;

    DataTable dt = new DataTable();

    dt.Columns.Add("RowNumber", typeof(int));
    dt.Columns[0].AutoIncrement = true;
    dt.Columns[0].AutoIncrementSeed = 1;
    dt.Columns[0].AutoIncrementStep = 1;

    da.Fill(dt);
    e.DataSource = dt;
}

WebGrid's column definition:

<ISWebGrid:WebGrid ID="WebGrid1" runat="server" Height="250px" UseDefaultStyle="True"
    Width="500px" RenderingMode="HTML5"
    OnInitializeDataSource="WebGrid1_InitializeDataSource">
    <RootTable DataKeyField="CustomerID">
        <Columns>
            <ISWebGrid:WebGridColumn Caption="Row Number" DataMember="RowNumber"
                Name="Row Number" Width="100px">
            </ISWebGrid:WebGridColumn>
            <ISWebGrid:WebGridColumn Caption="CustomerID" DataMember="CustomerID"
                Name="CustomerID" Width="100px">
            </ISWebGrid:WebGridColumn>
            <ISWebGrid:WebGridColumn Caption="CompanyName" DataMember="CompanyName"
                Name="CompanyName" Width="100px">
            </ISWebGrid:WebGridColumn>
            <ISWebGrid:WebGridColumn Caption="ContactName" DataMember="ContactName"
                Name="ContactName" Width="100px">
            </ISWebGrid:WebGridColumn>
            ...
        </Columns>
    </RootTable>
</ISWebGrid:WebGrid>

The result is:

Please allow me to assist you with the deployment problem one-by-one. First, let's start with the WebTreeView.

Everyting works fine on my development machine in all browser types (IE11, Chrome, FireFox).

During development phase, does the app (in development machine) uses SmartWebResources or not uses SmartWebResources? If the app in development machine doesn't use SmartWebResources then it would be as simple as xcopy the app to deployment server.

A simple WebSite with unbound WebTreeView is deployed to my IIS 8.5. Below is the settings which related to WebTreeView defined in web.config file.

<configuration>
  <appSettings>
    <add key="ISNet.WebUI.ISRes_Registered" value="false"/>
    <add key="ISNet.WebUI.v3_0_5000.OptimizeCss" value="true" />
    <add key="ISNet.WebUI.v3_0_5000.OptimizeCssName" value="true" />
    <add key="ISNet.WebUI.v3_0_5000.GroupCssStyles" value="true" />
    
    <!-- WebTreeView Settings -->
    <add key="ISNet.WebUI.WebTreeView.v1_0_1500.ImagesDirectory"
         value="~/CommonLibrary/Images/WebTreeView/"/>    
    <add key="ISNet.WebUI.WebTreeView.v1_0_1500.RenderingMode"
         value="HTML5"/>
    <add key="ISNet.WebUI.WebTreeView.v1_0_1500.RuntimeLicenseKey"
         value="RUNTI-MELI-CENSE"/>
    <add key="ISNet.WebUI.WebTreeView.v1_0_1500.ScriptDirectory"
         value="~/CommonLibrary/WebTreeView/V1_0_1500/"/>
    <add key="ISNet.WebUI.WebTreeView.v1_0_1500.SharedScriptDirectory"
         value="~/CommonLibrary/Shared/"/>
    <add key="ISNet.WebUI.WebTreeView.v1_0_1500.EnableWebResources"
         value="Never"/>
  </appSettings>
  ...
</configuration>

Note: the value shown at the above settings may differ/vary according to the configuration of deployment environment.

Please ensure that those settings have been configured properly. You can use the Network tool of IE 11 Developer Tool to determine which js files or images that missing (http404).

ISNet.ActiveReports.Exporting.dll is the assembly that is used by WebGrid's exporting feature. It can be found in "[Installation folder]\WebUI Studio for ASP.NET\WebUI.NET Framework 3.0\bin" folder. There is no newer version of this assembly yet. If any, it will be included in WebUI.NET Framework 3 updates.

ISNet.WebUI.WebDesktop.Resources.dll responsibles for context menu feature in WebGrid. As the assembly name stated, it is a part of WebDesktop and can be found in "[Installation folder]\WebUI Studio for ASP.NET\WebDesktop.NET 4.0\bin" folder. Updates will be included in WebDesktop.NET 4.0 hotfix.

Hope this helps.

The above screenshot shows my simple sample of WebContextMenu is rendered no IE 11 browser.

I enclosed the modified version of SimpleLayout.aspx (one of WebPaneManager sample) where WebButton and WebContextMenu are added into the Side pane. Please have the sample evaluated on your end and let me know if you have different result.