If you use Google Reader, you might find yourself seeing this choice screen a lot. Thankfully though there are ways to avoid it for those of us that only use Google Reader, rather than adding feeds to your iGoogle Homepage. There could be methods out there for browsers like Opera and Safari, though I'll just be covering Firefox and Chrome since they're arguably the two most-used browsers that aren't IE.
Firefox
Like a hack I posted to enable searching from Firefox's "Awesome bar", you can achieve this by modifying your about:config. Search for bro*.con and it'll filter down to a bunch of strings all starting with browser.contentHandlers.types.
Now find the entry for Google (mine is 0, yours could be something else) and update the matching uri value to be http://www.google.com/reader/view/feed/%s. When that's done, clear the value of browser.contentHandlers.auto.application/vnd.mozilla.maybe.feed (the top one) and restart Firefox. On the next launch it will repopulate that value with the new Google Reader URI. You could also simply overwrite the old value with the new yourself but you have to restart Firefox either way, so... whatever, really.
Chrome
I barely ever use Chrome these days since it doesn't quite fit my needs when it comes to tabs, but many people do. If you're one of them, there's an RSS Subscription Extension by Google that will add an RSS icon to the right of the location bar. Simply check the box to 'Always use this reader...' the first time you subscribe to a feed, and future subscriptions will go straight to Google Reader (unless you chose a different one, of course).
Revert! Revert!
If at some point you change your mind, you can go back to 'the old way' by simply removing the extension in Chrome. Alternatively, Firefox users can repeat the same steps as before but instead changing the URI back to http://fusion.google.com/add?feedurl=%s.
Source: superuser.com