Yep, every single one of them. Once again, Generation 1 isn't included, due to the legends having the regular Wild Pokemon battle music in that game. I'm also not using Mewtwo's theme due to its almost identical nature of the regular Legendary theme.
Pokemon Crystal Legendary Beast Theme
Pokemon R/S/E Deoxys Theme
Pokemon R/S/E Regi Theme
Pokemon R/S/E Groudon, Kyogre, and Rayquaza Theme
Pokemon FR/LG Moltres, Zapdos, and Articuno Theme
Pokemon D/P/Pt Dialga and Palkia Theme
Pokemon D/P/Pt Uxie, Mesprit, and Azelf Theme
Pokemon D/P/Pt Legendary Pokemon Theme (Giratina Altered Forme, Regigigas, Darkrai, Heatran, Rotom, Moltres, Zapdos, Articuno)
Pokemon D/P/Pt Arceus Theme
Pokemon Platinum Giratina Origin Forme Theme
Pokemon B/W Legendary Battle Theme
Pokemon B/W Secret Legendary Battle Theme
My personal favorite would have to be the Giratina theme from Platinum. The distorted instruments and techno sounds perfectly capture the unknown realm that you're fighting in, and the music also manages to capture Giratina's ferocious and possibly violent nature. Uxie/Mesprit/Axelf Theme is a close second.