Studying for the CCNA can be a daunting task. There are seemingly so many different websites, books, videos, and courses you can take that it's a whole workload just to sift through them all and find the best ones. Here is a list of resources that are top of the line. Using the following list of CCNA resources is more than enough to pass the exam with flying colors.
By far the number one resource you should have when studying for the CCNA is a good book. A book will go further in depth than any website but will also allow you to study at your own speed. You can review as often as needed, and at the end of every chapter a good book will have review questions and practice tests. The best CCNA book is going to be CCNA Routing and Switching Study Guide: Exam 100-105, Exam 200-105, Exam 200-125 by Todd Lammle. This is the book I personally used when I first passed the CCNA. If for some reason you do not want Lammle's book, CCNA Routing and Switching 200-125 Official Cert Guide Library by Wendell Odom is also highly recommended. Honestly, either one of the above books is going to set you on the fast-track to obtaining your certification, and will be useful as a reference in your career.
Along with a good book, you will need to some way to practice your IOS commands. Hands on practice will familiarize you with the commands and troubleshooting. You will inadvertently make mistakes setting up your test labs, and in doing so you will be forced to troubleshoot your test network until you figure out what went wrong. This is the closest you will be to actually troubleshooting in the real world. Packet Tracer has all the commands you will need for the CCNA and is easier to setup than GNS3. Of course, if you can afford it, there is no substitution for working with real networking equipment such as a CCNA Lab Kit.
To get Packet Tracer you must enroll in the Cisco Networking Academy, but there does seem to be a few places online where you can download the program for free. I won't link them because I don't know how legal they are, but if you are interested you can certainly find them on google.
A good book and a place to practice IOS commands is all you really need to pass the CCNA. It is all I used and I passed on my first attempt without any problems. However some students feel they need more. If that is the case, start with watching some videos. There is a good CCNA Training Series on Youtube which is free and just as good as most paid video courses.
Finally, when you are close to taking the test, do your best to find as many practice exams and simulation labs as you can. One of my co-workers used the CCENT ICND1 100-101 Flash Cards and Exam Practice Pack (Flash Cards and Exam Practice Packs), which was OK, but not amazing. They are for the previouse CCNA version, but are still useful for the current exam. Unfortunately there is no single great place to find lots of good practice questions for the CCNA. The best ones I found were in full books rather than on the Internet. If you are lucky enough to have access to more than one CCNA book, be sure to do the practice tests from all of them. You don't need to read more than one CCNA book, but going through multiple practice questions from different books can be very helpful.