It doesn't matter what you use as long as it's up to date and is not VLC. CCCP, K-Lite, Shark007, and KCP all work with .mkv files using most of (if not all) the same standard parts so you can even set it up yourself without using a pack made for casuals and get similar results.
If, for some reason, you are using VLC, remember to set your video output to OpenGL for proper levels.
The guides are outdated, but the information about Hi10P and the basic components, MPC-HC (Player) + LAV Filters (Splitter, Video, Audio) + xy-VSFilter (Subtitles) + madVR (Renderer), used most commonly aren't.
AzureHakua's "MPC-HC + LAV Filters + xy-VSFilter + madVR Guide" - Alternative to the first guide in case of prefering VSFilter instead of ISR.
The Anime Lounge Sticky - Downloading anime and manga by IRC.
imouto.my Blog Post - Watching h.264 videos with DXVA. Warning: the site is a clusterfuck.
imouto.my Blog Post - Watching h.264 videos with CUDA. Also has options for software decoding, DXVA and Intel QuickSync.
MangaUpdates RSS - RSS feed to keep up to date with the latest translated chapters of the manga you are reading. Yahoo Pipes has been retired.
Don't use Mangafox or Mangahere, use Batoto or something else that doesn't shit on the pages with watermarks and compression.