Assuming V2+ of the .Net framework :
If you're publishing a website you can just upload the files that you changed, via FTP say as long as the site was published with 'Allow this precompiled site to be updatable' when you did the publish (or in the property pages of the website in VS2008).
This isn't quite the case with web applications, which will need you to deploy any changed assemblies again. Your aspx and ascx files, however can be reuploaded, obviously its best not to do this incase you break something without realising.