Tegamibachi Reverse

both about sending messages and issues of love and war 

both of the main character's mom died/ taken away an evil organization wants to take over the capital city main character finds their long lost dad/friend 

Strong children as main characters, both with magical eyes and a gloomy atmosphere around 

Both have silver haired bishounen who are passionate about their line of work. Both boys have one eye that is activated when in a battle: for LB its battling gaichuu and for DGM its demons. Both Lag and Allen are orphans and have someone who influenced them.  

Both are sequels of previous anime. (So you must watch the prequels to understand.) Both focus on the protagonist, (Sakura in Tsubasa, Lag in Letter bee) searching for and trying to return the "heart" of the person they cherished the most, a person who was very kind and gentle, but then lost his heart and became cold, without memories, becoming an "enemy". While in Letter bee, Letters and bullets contain memories and are made of heart, in Tsubasa, Sakura´s heart are feathers of memories. Although, Letter bee is slice of life, and Tsubasa is drama & Romance.  

Both main characters are little boys with big ambitions and a lot of heart. Both are always going out of their way to help others and care a lot about the people who support them. Both boys also have to learn, from square one, how to take care of themselves and fight monsters/spirits. Mokkun (SO) and Niche (TB) also share the Pet/Protector element. If you like Tegami Bachi Reverse, I think you'll love Shounen Onmyouji! 

Lag was finding Gauche while Haseo was searching for Ovan. both Lag and Haseo idolized Gauche and Ovan. and as the story developed, both of the main characters tried to be more powerful to protect their friends.