How to write Unit Tests for Web Applications and Controls

I would test the application base class indirectly by creating a subclass and testing that, just as you said.

For the controls, I would use Selenium: http://selenium.seleniumhq.org/.

It's no longer maintained but there is NUnitAsp.

[Test] 
public void TestExample() 
{ 
   // First, instantiate "Tester" objects: 
   LabelTester label = new LabelTester("textLabel"); 
   LinkButtonTester link = new LinkButtonTester("linkButton"); 

   // Second, visit the page being tested: 
   Browser.GetPage("http://localhost/example/example.aspx"); 

   // Third, use tester objects to test the page: 
   Assert.AreEqual("Not clicked.", label.Text); 
   link.Click(); 
   Assert.AreEqual("Clicked once.", label.Text); 
   link.Click(); 
   Assert.AreEqual("Clicked twice.", label.Text); 
}

This is only a partial answer. This is the way you'd do this type of a thing in Django. I imagine there is something similar in ASP.NET. For testing the client-side code there are things like jsUnit.

I was able to do this by creating a stub for the web control that I am unit testing, and calling the protected RenderContents() method, and validating the HTML:

[Test]
public void ConditionQueryBuilderTest_RendersProperHtml()
{
    var sw = new StringWriter();
    var queryBuilder = new ConditionQueryBuilderStub
    {
        ID = "UnitTestbuilder",
        QueryBuilderURL = @"\SomeAspxPage\SomeWebMethod",
        ResetQueryBuilderURL = @"\SomeAspxPage\OnQueryBuilderReset",
        FilterValuesCollection = new Dictionary<int, string> { {15, "Some Condition"}}
    };
    queryBuilder.RenderAllContents(new HtmlTextWriter(sw)); // This is a method in my stub that exposes RenderContents()

    AppendLog(sw.ToString());

    Assert.AreEqual(ExpectedHtml, sw.ToString());
}