SPWebConfigModification

public override void FeatureActivated(SPFeatureReceiverProperties properties)
{
	var webapp = parent as SPWebApplication;
	if (webapp != null)
	{
		var mod1 = GetWebControlsConfigMod();
		webapp.WebConfigModifications.Add(mod1);
		var mod2 = GetConStringConfigMod();
		webapp.WebConfigModifications.Add(mod2);
		SaveChanges(webapp);
	}
	else
	{
		Log.Warning("no modifications to webapp are done");
	}
}

public override void FeatureDeactivating(SPFeatureReceiverProperties properties)
{
	var webapp = parent as SPWebApplication;
	if (webapp != null)
	{
		var mod = GetWebControlsConfigMod();
		var modsCollection = webapp.WebConfigModifications;
		var modToDelete =
			(from m in modsCollection
			 where m.Value.Equals(mod.Value, StringComparison.InvariantCultureIgnoreCase)
			 select m).FirstOrDefault();
		if (modToDelete != null)
		{
			modsCollection.Remove(modToDelete);
			SaveChanges(webapp);
		}
	}
}
private static void SaveChanges(SPPersistedObject webapp)
{
	var service = webapp.Farm.Services.GetValue();
	service.ApplyWebConfigModifications();
	webapp.Update();
}

private static SPWebConfigModification GetWebControlsConfigMod()
{
	var assembly = System.Reflection.Assembly.GetAssembly(typeof(WebControls.OfficeEditor));
	var ass = assembly.FullName;
	var @namespace = assembly.GetName().Name + ".WebControls";
	var value = string.Format("", ass,
							  @namespace);
	const string path = "configuration/SharePoint/SafeControls";
	var mod = new SPWebConfigModification
	{
		Path = path,
		Name = "JustaName1",
		Sequence = 0,
		Owner = @namespace,
		Type = SPWebConfigModification.SPWebConfigModificationType.EnsureChildNode,
		Value = value
	};
	return mod;
}

private static SPWebConfigModification GetConStringConfigMod()
{
	const string name = "ContosoConString";
	const string conString =
		"Data Source=db.contoso.com;Initial Catalog=contoso\_db;Persist Security Info=True;User ID=contoso\_Contributor;Password=contoso";
	var mod = new SPWebConfigModification
	  {
		  Name = "JustaName2",
		  Path = "configuration/connectionStrings",
		  Owner = "contoso\_connectionstrings",
		  Type = SPWebConfigModification.SPWebConfigModificationType.EnsureChildNode,
		  Value = String.Format("", name, conString)
	  };
	return mod;
}

#ADDING
asnp microsoft.sharepoint.powershell
$url = "http://contoso"
$app = Get-SPWebApplication $url
$name = "ContosoConString";
$conString = "Data Source=db.contoso.com;Initial Catalog=contoso\_db;Persist Security Info=True;User ID=contoso\_Contributor;Password=contoso";
$mod = new-object Microsoft.SharePoint.Administration.SPWebConfigModification
$mod.Name = "JustName2"
$mod.Path = "configuration/connectionStrings"
$mod.Owner = "User Name"
$mod.Type = 0 #for the enum value "SPWebConfigModification.SPWebConfigModificationType.EnsureChildNode"
$mod.Value = '<add name="{0}" connectionString="{1}" />' -f $name, $conString
$app.WebConfigModifications.Add($mod)
$service = [Microsoft.SharePoint.Administration.SPWebService]::ContentService
$service.ApplyWebConfigModifications()
$app.Update()
#ADDING snapin
asnp microsoft.sharepoint.powershell

$url = "http://contoso"
$app = Get-SPWebApplication $url

#SafeControl
$assembly = "Contoso.SP, Version=1.0.0.0, Culture=neutral, PublicKeyToken=20c0327f8b01d979"
$namespace = "Contoso.SP.WebControls"
$mod = new-object Microsoft.SharePoint.Administration.SPWebConfigModification
$mod.Name = "ContosoSafeControls"
$mod.Path = "configuration/SharePoint/SafeControls"
$mod.Owner = "Contoso"
$mod.Type = 0 #for the enum value "SPWebConfigModification.SPWebConfigModificationType.EnsureChildNode"
$mod.Value = '<SafeControl Assembly="{0}" Namespace="{1}" TypeName="\*" Safe="True" />' -f $assembly, $namespace
$app.WebConfigModifications.Add($mod)

#applying changes
$service = \[Microsoft.SharePoint.Administration.SPWebService\]::ContentService
$service.ApplyWebConfigModifications()
$app.Update()

#REMOVING
asnp microsoft.sharepoint.powershell
$app = Get-SPWebApplication http://contoso
$modCol = $app.WebConfigModifications
$mod = $modCol| Where { $\_.Owner.Equals("User Name") }
$modCol.Remove($mod)
$service = [Microsoft.SharePoint.Administration.SPWebService]::ContentService
$service.ApplyWebConfigModifications()
$app.Update()

#if you want to clear all web.config mods associated with the web app:
$modCol = $app.WebConfigModifications
while ($modCol -ne 0) { $modCol.Remove($modCol\[0\]) }
$service.ApplyWebConfigModifications()
$app.Update()