Young boy protagonist with a sword containing a red stone on its hilt?
I think it could be Shin Hakkenden (1999, 26 episodes)


  The year is 2588 in the system of Godworld and its eight satellites. Humanity came here in the distant past, after a long journey across the stars from Earth. Now the system is ruled by a loose coalition of powerful families: House Owari, House Meed, and House Iigy. The story begins when Kai, the heir to House Owari, attacks an icy planet. Living in a humble village on the surface is Kou, a young boy who is perpetually arguing with his father. When Kai's navy arrives, Kou takes his father's mighty Murasame sword to fight back, and his adventures begin. A sci-fi remake of Hakkenden. (Plot from Animevice).


This is a picture of the main character Kou who has a red gem in his sword (You can also see a dog with an eyepatch: it hide a yellow gem in one of his teeth).



This is Jinrai who has a green gem in his shield.

Another pic http://gallery.animeinfo.ru/img/Jinrai-125835-57413-1.jpg

This is Tomoka who has a blue gem in a dice: he is a gambler and use cards also for fighting.