I think to really look at the differences between web sites and software programs we need to define them. There are exceptions to everything and if you don't define users interaction with both, you will be side tracked on these exceptions.
Web Site - A web site is a collection of information contained on the Internet for the general public to interact with (this is a basic generalization of information sites. If we start to get into ecommerce, web reporting, and applications they should start to follow a hybrid of both web and software usability.).
Application Software - A desktop application is a program run locally on a client machine that performs tasks for the user.(Again this is a generalization to simplify our discussion).
So why don't we start a list that everyone can add to?
Web Site Usability
1.A web site information should be obvious and easy to get to.
2.A web site's navigation should be clear about where each link will take you at a glance.
4.A web site should load quickly to help users get the information from the site in a timely manner.
5.Users should decide what pages they want to see on a web site and not be hijacked by the browser’s content.
6.Any terms of service, privacy policies, or other important information for the user should be put in a conspicuous place for users to easily find and read.
8.Web sites should work with all common browsers and operating systems. There is a common set of markup that works on all common browsers. It is possible to insure that a sight works and looks properly across platforms and browsers. Making sights that only work in a certain operating system or browser destroys usability for users without your requirements.
9.Any aspect of the site that does not enhance usability or the general focus of the content is extraneous and should be excluded.
Application Software Usability
1.Application software should perform its tasks flawlessly on all systems that are covered by its requirements. Example: Many games change color depth on a computer to 256 colors. An application with 256 colors included in its requirements should not remove subtle colors informs and tables.
2.Users should have at least to ways to perform operations in an application. Use of the file/edit bar and a toolbar (floating and nonfloating). Applications should also allow advanced users to quickly perform its operations. It is also recommended that applications include hot key or keyboard shortcut operations for common tasks. Right click (apple click or secondary clicking) menus are recommended to include operations associated with the element click on.
3.Operation icons should include tool tips (hover information of the operation similar to alt tags attributes for images), a legend, or text labels identifying the action performed by clicking it.
4.All elements should allow operating system preferences to be used. Operating system themes should be able to hook into the application.
5.Software installation should include all necessary information for the program to run.
6.All icons should have a consistent look throughout the application based on the common application visual language. This also includes cursors for drag drop and other mouse events.
7.Applications should include searchable help through the application interface.
8.Any problems that occur within the application should notify the user what happened.
9.Basic operating system commands like cut and paste should be available in the application.
1.All form fields should be validated.
2.Input fields should have sequential and obvious tab order.
3.Niether should inhibit normal operating system functions.
4.Niether should interact with other applications or programs without users consent.
5.Niether should damage the user's machine or other information on their machine.
6.Actions should be clearly labeled and do what they say.
These are just some basic usability guidelines. There are exceptions to each rule, but if followed can give your users a better experience.