Fire up Xcode and select Build -> Build and Archive. The Organiser will pop-up. Select the build you want to publish and click on the Share... button above the list. Select then the identity you want to sign your code with (usually this is the same you use for signing the code for a standard deploy on the device). Click, then, on Distribuite for Enterprise..
At this point a form will appear asking you from which URL the application should be downloaded from. Let’s suppose your website is available at www.example.com and your application (the file .ipa) is hosted at www.example.com/download/myapp.ipa, then http://www.example.com/download/myapp.ipa should go in that field. [See the update below]
Fill the other fields as you wish; you can get more information about that in the Apple Documentation
Once you filled the form and clicked OK select the place where to save the generated files (ipa and plist).
Now the tricky parts comes when you have to deal with the webserver-side code. I have created a small example page below.
Remember that you have to put on your website all the files: myapp.ipa, myapp.plist and myapp.mobileprovision.
<!DOCTYPE HTML>
<html>
<head>
<title>Install your application</title>
</head>
<body>
<ul>
<li> <a href="http://www.example.com/download/myapp.mobileprovision">Install Team Provisioning File</a></li>
<li><a href="itms-services://?action=download-manifest&url=http%3A%2F%2Fwww.example.com%2Fdownload%2Fmyapp.plist">Install Application</a></li>
</ul>
</div>
</body>
</html>
Please notice that the second href is nothing just a plain old-fashioned URL. Nothing special into that. If you are wondering about those weird %2F and %3A they are normal urlencoded symbols (for ‘/’ and ‘:’ resp.).
Once you did this you are definitely done.
This answer has been taken as part of a blogpost I made in 2010. You can read the full story here