ASP.NET 1 and 2 can not work on a same domain. However, if you want to use ASP.NET 2, 3.0 and 3.5 on a single domain then you just need to place separate web.config files by changing the target framework version(compiler version) accordingly. Find the below code and change the Version=2.0.0.0, 3.0.0.0 accordingly. Moreover, you need to keep only one BIN directory at the root application directory.
<assemblies>
<add assembly="System.Core, Version=3.5.0.0, Culture=neutral, PublicKeyToken=B77A5C561934E089"/>
<add assembly="System.Web.Extensions, Version=3.5.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35"/>
<add assembly="System.Xml.Linq, Version=3.5.0.0, Culture=neutral, PublicKeyToken=B77A5C561934E089"/>
<add assembly="System.Data.DataSetExtensions, Version=3.5.0.0, Culture=neutral, PublicKeyToken=B77A5C561934E089"/>
<add assembly="System.Web.Extensions.Design, Version=1.0.61025.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35"/>
<add assembly="System.Design, Version=2.0.0.0, Culture=neutral, PublicKeyToken=B03F5F7F11D50A3A"/>
<add assembly="System.Web.Extensions, Version=1.0.61025.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35"/>
<add assembly="System.Windows.Forms, Version=2.0.0.0, Culture=neutral, PublicKeyToken=B77A5C561934E089"/>
</assemblies>
<compilers>
<compiler language="c#;cs;csharp" extension=".cs" type="Microsoft.CSharp.CSharpCodeProvider,System, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" warningLevel="4">
<providerOption name="CompilerVersion" value="v3.5"/>
<providerOption name="WarnAsError" value="false"/>
</compiler>
<compiler language="vb;vbs;visualbasic;vbscript" extension=".vb" type="Microsoft.VisualBasic.VBCodeProvider, System, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" warningLevel="4">
<providerOption name="CompilerVersion" value="v3.5"/>
<providerOption name="OptionInfer" value="true"/>
<providerOption name="WarnAsError" value="false"/>
</compiler>
</compilers>