After Naruto Shippuden 53, All of the files are in HD and can be played with VLC player, with no additional codecs needed. Please note that VLC is a PLAYER, and not a "CODEC PACK", therefore after installing it you will need to use it to play back the file, not the player you used prior to installing VLC. (If the episodes do not play on VLC, then the issue is with your system and we really can't help you there)
Or, you can download and install the proper codec.
Naruto episodes up to and including Naruto Shippuuden 53 are encoded with XViD. They will also play if you install ffdshow. Naruto Shippuuden episodes from 54 on are encoded with h.264. You will need a h.264 decoder installed. Tailedfox strongly recommends using Media Player Classic - HomeCinema for playing back h.264 material as the required decoder is built in, and does not require installation of any external codec packs. Alternatively, for slow systems, CoreAVC decoder is recommended for playback. This decoder is not free. Tailedfox does not support or recommend installing "codec packs" in order to view them.