One common theme is redemption. Merle has a complex character, and often in these fanfictions, the relationship with the OC helps him find a better version of himself. Another theme is survival. Given the 'The Walking Dead' setting, both Merle and the OC have to fight to stay alive, and their relationship is tested in the face of danger. Love is also a major theme, as the fanfictions explore how two very different characters can fall for each other in such a harsh world.
Some 'Merle Dixon x OC fanfiction' that I think are worth checking out are those that explore different sides of Merle. For example, 'The Hidden Side of Merle Dixon x OC' delves into Merle's past and how the OC helps him come to terms with it. 'Merle Dixon x OC: Allies to Lovers' is a story that shows their relationship evolving from being just comrades in a tough situation to something more romantic. There's also 'In Merle's Shadow: The OC's Story' which focuses on the OC's perspective while being in a relationship with Merle, and how she copes with his often - difficult personality.
One popular theme is redemption. Given Merle's rough and often unlikable character in the original, many fanfictions explore his journey towards redemption. Another theme is family, perhaps exploring his relationship with Daryl in different scenarios. Survival is also common, as it was a major aspect of the show he's from. Fanfictions might show Merle using his skills in new and different survival situations.