Wild ARMs has some songs that are popular but the series as a whole has some fine tunes.
Wild ARMs. Michiko Naruke's amazing compositions are frequently cited as one of the best aspects of the series. On the softer side, there's: the first game's intro, Into the Wilderness, the second game's intro, You'll Never Be Alone, and Rudy's theme from the first game (which unfortunately doesn't appear to be easily found on Youtube). There are also several amazing boss themes, including Zed, Boomerang Flash, and Janus.
And Wild Arms 2 has one of the best standard boss themes.
If we're going the talk about Boomerang Flash, we should probably also mention his theme from the Updated Rerelease, War Demon. Which plays now during ALL of his battles. And is awesome.
Wild Arms Alter Code: F, the Playstation2 Remake of the original game, has a whole new OST with some remixed songs from the first game and some original songs.
Wild ARMs 3 has more awesome tunes, particularly "FATE Breaker" and "Flying in the Mists of the Storm", though there are several dozen tracks that would easily fit this category. The ending theme, Wings, has cemented its place as the best ending song of any game, ever (only the one used in the US, though; the Japanese version is nowhere near as powerful, and the version in the US game is not available on any soundtrack; it has to be ripped from the game OST.)