I've only recently gotten into Merlin fic too and I've read some really amazing stories.

Two of my favorites (of which there are many) are these two, which are Merlin/Arthur if you don't mind that pairing, their relationship develops along with the plots nicely;
The Tournament of All Magicks and The Crown of the Summer Court. The Magic and story and adventure in these are amazing and riveting.

I also stumbled across a Rec list of rec lists. Most look to be Merlin/Arthur as well but there's a few that list other/all pairings and gen.

Have fun!