In reply to Robert Lavin:
Hi Rob
Apparently my partner works (Naomi Dalton) with your partner so I'd be more than happy to meet up and give you some advice in person. I lived in Chile for 8 months and did various bits and pieces while I was there.
Here is a trimmed down version. With only three or four weeks I'd spend all my time in Patagonia. Chile is a stunningly beautiful country but Patagonia is undeniably the jewel in it's crown. Torres Del Paine as mentioned above is the most popular place, with good reason. It can easily be combined with Fitz Roy in Argentina as well. You would probably want to do multi-day backing packing there.
In the north of Patagonia there are lots of options from Puerto Montt and nearby for both easy peaks and multi-day treks. The opportunities available are huge and you should be able to get away from the crowds if you desire. Again treks can be linked with Argentina which is most popular via Bariloche .
I have a soft spot for central Chile as it's where I did most of my trekking and your unlikely to see many foreigners but it's probably not as impressive as the stuff further south. There are lots of options and I never needed a permit for anything I did nor heard that it was necessary.
I turned down a job in the north in San Pedro de Atacama and consequently never visited that region. From what I've heard from others the Bolvian side is more worth visiting. Tours are generally down by jeep as you generally need to carry all your own water although there are various peaks that can be climbed. I had a friend who visited a year or so back who would know more.
This website was created by a friend and very useful, especially if you can speak Spanish. There are some English articles written by me and others by Chileans in their second language:
http://www.wikiexplora.com/index.php/Trekking_Chile
If you are planning something particularly adventurous I can get in touch with Joaquin or people at the German mountaineering club (DAV) who would be more helpful
This website is excellent.
http://www.trekkingchile.com/indexEN.html
In terms of books the lonely planet is good for just Patagonia and the Bradt guide to trekking in Chile is good for the whole country, including stuff in the north. Unfortunately I gave it to a friend in Chile. I do however still have a very rare copy of adventures in central Chile if you were planning on going to that region, a beautifully researched and produced book which is useful to almost no-one. Finally I have created a google map of Chile with all the information from my guidebooks on it which I could share with you as well.
Post edited at 22:57