Modify SharePoint web.config using object model....

Root Level Web.Config

  <appSettings>
    <add key="AppKey" value="AppValue"/>  </appSettings>

Code Snippet

using System;using System.Configuration;using System.Web.Configuration;

namespace SampleApplication.WebConfig
{
    public partial class webConfigFile : System.Web.UI.Page    {
        protected void Page_Load(object sender, EventArgs e)

        {
            //Helps to open the Root level web.config file.            Configuration webConfigApp = WebConfigurationManager.OpenWebConfiguration("~");

            //Modifying the AppKey from AppValue to AppValue1            webConfigApp.AppSettings.Settings["AppKey"].Value = "AppValue1";

            //Save the Modified settings of AppSettings.            webConfigApp.Save();        }
    }
}

Output of Root Level Web.Config:

 <appSettings>
    <add key="AppKey" value="AppValue1"/>  </appSettings>

In order to modify application specific web.config entry below is the code snippet:

using System;

using System.Reflection;

using Microsoft.SharePoint.Administration;

namespace SharePointLiveForMe.SharePoint.Administration

{

    /// <summary>

    /// This class allows to add or remove entries in web.config.

    /// </summary>

    public class WebConfigManagement

    {

        /// <summary>

        /// This methods allows to add a key/value pair in the AppSettings section.

        /// </summary>

        /// <param name="Key">Name of the key</param>

        /// <param name="Value">Value</param>

        /// <param name="webApp">Web application</param>

        public static void AddAppSettingsKeyValue(string key, string value, SPWebApplication webApp)

        {

            if (!string.IsNullOrEmpty(key) && !string.IsNullOrEmpty(value) && webApp != null)

            {

                SPWebConfigModification modification = GetModification(key, value);

                //Add app setting key value if it is not there in web.config file 

                if (!webApp.WebConfigModifications.Contains(modification))

                {

                    webApp.WebConfigModifications.Add(modification);

                    webApp.Farm.Services.GetValue<SPWebService>().ApplyWebConfigModifications();

                    webApp.Update();

                }

                else

                {

                    //modify existing entry
                    webApp.WebConfigModifications.Add(modification);

                    webApp.Farm.Services.GetValue<SPWebService>().ApplyWebConfigModifications(); 

                    webApp.Update();

                } 

            }

            else

                throw new ArgumentNullException();

        }

        /// <summary>

        /// This methods allows to remove a key/value pair in the AppSettings section.

        /// </summary>

        /// <param name="key">Name of the key</param>

        /// <param name="value">Value</param>

        /// <param name="webApp">Web application</param>

        public static void RemoveAppSettingsKeyValue(string key, string value, SPWebApplication webApp)

        {

            if (!string.IsNullOrEmpty(key) && !string.IsNullOrEmpty(value) && webApp != null)

            {

                SPWebConfigModification modification = GetModification(key, value);

                if(webApp.WebConfigModifications.Contains(modification))

                {

                    webApp.WebConfigModifications.Remove(modification);

                    webApp.Farm.Services.GetValue<SPWebService>().ApplyWebConfigModifications();

                    webApp.Update();

                }

            }

            else

                throw new ArgumentNullException();

        }

        /// <summary>

        /// This method allows to build an SPWebConfigModification object.

        /// </summary>

        /// <param name="key">Name of the key</param>

        /// <param name="value">Value</param>

        /// <returns></returns>

        private static SPWebConfigModification GetModification(string key, string value)

        {

            if (!string.IsNullOrEmpty(key) && !string.IsNullOrEmpty(value))

            {

                SPWebConfigModification modification = new SPWebConfigModification();

                modification.Name = string.Format(@"add[@key=""{0}""]", key);

                modification.Path = "configuration/appSettings";

                modification.Value = string.Format(@"<add key=""{0}"" value=""{1}"" />", key, value);

                modification.Owner = Assembly.GetExecutingAssembly().FullName;

                modification.Sequence = 0;

                modification.Type = SPWebConfigModification.SPWebConfigModificationType.EnsureChildNode;

                return modification;

            }

            else

                throw new ArgumentNullException();

        }

    }

}