My superiors decided that they want to use the ASP.NET Portal Starter Kit, before they realized we should have a real business logic layer and do O/R mapping. They found a whitepaper about it on MSDN dated 2002. Its "framework" (more like a loose template) expects you to create a DAL that takes and returns DataSets, gives examples of doing your CRUD with stored procedures, and has no querying capability beyond getting a single entity by ID or getting all of them.

Should I go along with them and shoehorn NHibernate into this framework, or can we ditch it for something much better? We haven't actually written anything yet.

When I asked where they got the whitepaper on the Portal Starter Kit, they tried to show me, but Microsoft removed the link. Apparently it's obsoleted by .NET 2.0? We found no obvious .NET 2.0 replacement on MSDN ...

You have to decide what's important for you. Do you want lots and lots functionality out of the box, just go and download DotNetNuke. Technically it's not my cup of tea, but it has a very vibrant community and is extremely well supported.
If you want something with NHibernate, check out Cuyahoga (shameless plug). It doesn't offer that much out of the box, but if you're going to do lots of custom work, it might be interesting.
Just don't touch the Portal Starter Kit, because you have to invest way too much time to clean up the architectural mess.

Thanks for the insight. My bosses said they will consider each of them. Where does "Atlas" fit into all this? (Sorry if this is a stupid question, I'm a Windows Forms guy, and web moron ...)

Hmmm... Looking at DotNetNuke, it does not look like it will play nice with NHibernate. We do not want to give up O/R mapping. Does that eliminate DotNetNuke then?

Yes, that eliminates almost all solutions, but are you going to do a lot of custom work with it? If not then it doesn't matter (at least to me).

Atlas is your ajax framework written by Microsoft for asp.net 2.0 So what Atlas provides you is simplification of using ajax and hopefully in future easy deployment via the rad VS IDE.

You also have other options available, such as the free/commercial ajax.net http://ajax.schwarz-interactive.de/csha ... fault.aspx (which has recently stopped updates).

You've also got cool controls with ajax style functionality from http://www.telerik.com

All of these can hopefully be added to your portal solution where necessary. So hopefully your google ajax style keyword lookup search could be added to dotnetnuke, MojoPortal, or my favourite Cuyahoga which already is using NHibernate.