I've started two separate google reader accounts because I want to browse them in different ways. One contains news, and I want to be able to fly through that stuff and have it marked as read automatically. The other account is podcasts and I don't want those marked as read until I'm done with them. So, I have two accounts that use different behavior.
Here are the steps I performed to create multiple profiles using Google Chrome, allowing me to have quick access to two Google Reader setups. (I found a description of how this is done here)
Step 1: Clear browsing history and data (if you want to)
Step 2: Copy folder "C:Users[username]AppDataLocalGoogleChromeUser DataDefault" to a new folder in the same location (I called mine Podcasts)
Step 3: Set new profile to factory settings (if you want to) by running c:Users[username]AppDataLocalGoogleChromeApplicationchrome.exe –user-data-dir="C:Users[username]AppDataLocalGoogleChromeUser DataPodcasts" -first-run
Step 4: Create an app shortcut for Google Reader using Chrome and edit it to add the –user-data-dir= directory from above.
Now I have a shortcut (that I put in the Start Menu) I can use to get right at my podcasts…no browser navigation or passwords necessary. Once that profile has the right cookies it just works!