i assume you are passing the affiliate code in the query string or elsewhere in the url.
if target="_blank" typically munged urls it would be a huge problem in general - not just for affiliate urls.

erghhh... bland un-specific remarks don't help much in explaining the faults in doing so.

As much as you say this, many other webmasters could reply along the lines of "ohh, i've been using "target=_blank" for years with my affiliate links"......no negative issues.

ok then name something specific that could explain in technical terms what actually "went wrong".
when you click a link, the browser sends a request and a server sends a response.
there's no magic involved.

How 'bout this way: The server doesn't know that you said "target = '_blank'". The server only knows that there was a request and, optionally, that the request came with a referer.

It's pretty exactly the same principle as clicking on a fragment link on a page you're already on. (The server can send fragment links, but it doesn't receive them. Information in query strings doesn't count.) The "target = '_blank'" statement is used only by the browser.

Now, if you're doing something javascript-based, the code might be able to detect that the request is going into a new window. Note that I'm not saying it does or doesn't, I'm saying it is theoretically possible. But you'd have to look at the specific code to tell. The advantage of javascript for your purposes is that it's right in the page source-- either the code itself or a link to where it lives. So there shouldn't be any obstacle to snooping.

could [anything] screw up the tracking code from affiliate programs?

since i made an assumption and you didn't confirm or deny that assumption let's try to be more specific.
how are you providing the tracking code to your affiliate program?

Good explanation, Lucy.

Phranque, it's different with each program.

But generally something like :

<a href="http://www.example.com/ct/254812?b=1381" target="_blank" rel="nofollow">

[edited by: phranque at 2:44 am (utc) on May 20, 2013]
[edit reason] exemplified affiliate url [/edit]

i'm still assuming you are passing the affiliate code in the query string.
the HTTP Request as seen by the server would be identical with or without a target specified for the anchor tag.

But generally something like:

Are you passing along all of this information, or just the URL?