Great ruby on rails examples of almost real world applications: Can somebody give some links of sites that have such codes using the best practices in structure, implementing it, models, controllers, security, views, caching, modularizing and so on? thanks
You could start with guides.rubyonrails.org. They have a lot of information on there. A very good example to start with. Start with the Getting Started link. There are also a lot of other examples on that site.
The next step you might be better off buying a book on this subject. I purchased Simply Rails 2 by Patrick Lenz. Also a very good starter book with good examples. He walks you through an app that's similar to Digg. This will get you into the Model-View-Controller mind set.
If you want to go further, I would suggest Agile Web Development with Rails, Third Edition by Sam Ruby, Dave Thomas, David Heinemeier Hansson. I would suggest the PDF because I use it as a reference and searching within the 774 pages is helpful to say the least. This is my favorite but definitely not a starter book. It's broken into two halves. The first half is a tutorial on how to write a shopping cart. With this example you get into the database models, migrations, sessions, helpers, ajax, routes, security - shows you how to create your own authentication process and more. The second half of the book is more of a reference guide and goes into greater depth than the application tutorial.
From here I would look into plugins to help you out. Search on www.github.com. They host a lot of the open source plugins available. Don't go too wild on plugins because too many will defeat the principles of being RESTful. For security/authentication I would reccomend Authlogic. I still think it's beneficial to go through the tutorial on how to create your own authentication (from the Agile Web Development with Rails book) to see what actually goes into this plugin.
Lastly, but not the least bit important is to start thinking about how you will deploy your app. You may think this is trivial but the longer you put it off, the harder it will become. Look into capistrano and deprec gems (plugins) to deploy onto a VPS. I've had numerous problems deploying to a shared host.
Don't start with the most complicated part of rails like I did. Work from the guides first and get into more complicated apps. Rails has a pretty steep learning curve.
Hope this helps.
Found your post while I was looking for the same thing, this blog post was useful: http://blog.chrislowis.co.uk/2010/05/31/five-rails-apps-to-study-and-learn-from.html