I was wondering if anyone could provide some insight to this question.

We are considering offering and affiliate program for our hosting company. But can you build link pop with an affialite program if the linking is correct?

The closest that we have seen after looking is a url like this http://www.merchantsite.com/product1.htm?kbid=1001 our domain would replace merchantsite.com. This is just an example The link would go to our home page or to an informational page.

I know that SE's do not really like the question mark. But since it is after the .htm would it matter?

This is the summary of the email we recieved about this.

Affiliates can link directly to any page on your site. The key is this: each page of your site will have some html code on it that will determine if the visitor came from an affiliate or not, and will cookie the visitor upon landing on your web pages, as opposed to clicking through a tracking system first.

Will this work?

I'm not sure if serach engines bother too much about that, they might just ignore it completely. I know that Google will accept pages with question marks, but you may be better not having them.

One method you could try is to use a feature of Apache (which I've forgotten the name of... sorry) where it 'reads back' a URL if a file is not found. So you can have your URLs as:
http://www.yoursite.com/signup/1001
where the page is actually called signup and 1001 is the affiliate ID. I use it on Free Webmaster Help, for example:
http://www.freewebmasterhelp.com/tutorials/php/4
is actually a file called tutorials, and the script takes the name of the tutorial and the part from the URL. Very useful.

I think there was an article on Sitepoint describing how to do it.