asp.net CodeBehind vs CodeFile

Applicable to ASP.Net 2.0 onwards

if it is a "web application" project - use CodeBehind
if it is a "website" project - use CodeFile

in regular ascx file:

<%@ Control Language="C#" AutoEventWireup="true" Inherits="My.Great.Web.SomeCtrl" CodeBehind=SomeCtrl.ascx.cs" %>

in regular aspx file:

<%@ Page Language="C#" AutoEventWireup="true" Inherits="My.Great.Web.SomePage" Codebehind="SomePage.aspx.cs" %>

in global.asax:

<%@ Application Language="C#" Inherits="My.Great.Web.Global" CodeBehind="Global.asax.cs" %>

More info here: ASP.NET Web Page Code Model