Alex described how to use cookies for logging in to NYT. Some people had the problem that the cookies expired occasionally.
I found another way to login to NYT which always works

:
http://www.nytimes.com/auth/login?is_continue=true&OQ=&USERID=
<username>&PASSWORD=
<pwd>&log=Log+In&SAVEOPTION=YES&URI=
<urltoarticle>
<username> = your login username
<pass> = your login password
<urltoarticle> = the actual url to the nyt article or page that you want to download with isilox and that requires registration
Note that you don't have to fuss about cookies this way.
Updated: Url now working!
Updated again: Url *really* now working!
Enjoy!