After reading all the previous sections, you have covered but the very basics. The real specifics that you need to build cool applications are out there. In the following I attempt to point out some links, with the intention of adding more as time goes by.
If you'd like to add a link, contact anyone at http://hofmeyr.de
Here is an invaluable source of technical information around C for the AVR.
The manual used to be part of the source distribution of avr-libc, but now it is distributed separately. Check out the avr-libc download area for the user manual files. You'll probably want the html version.
There is a link to the avr-libc download area on the Installation instructions page.
Datasheets are absolutely essential. Get the ATMEGA datasheets from the ATMEL homepage, or, generally, running a search on the component's label should eventually get you a datasheet for that component, usually in PDF format.
Another good way to find datasheets for components is searching a component vendor site, like farnell.com.
A package of examples I extracted the Makefile from. Look for it on the web.
A Europe based website that has a lot of information and offers to sell components and ready built ISP cables.
This components shop in Berlin is truly magic. It is bigger from the inside than from the outside. If you happen to live in Berlin (Germany), be sure to skip all the places like Conrad or Atzert that keep giving you low quality components and bad service, and rather go directly to Segor. What a great shop!