For me, the most underrated song by them could possibly be Koi Moyou. It's not my favorite, but they never played it live after their first one-man live. It's still a good song, though, because it's simple and catchy at the same time. Easy to play too.
But I also have to agree with everyone else with Kimi to Yoru to Namida. That song has been stuck in my head. It's really nice. But a few other underrated songs are: Shining Sun, Hikare, Playboy Part 2, Pinheel Surfer (just a little, it's not bad, not great...), Yumemiru Tsubasa (same as Pinheel), Want You, Tokyo, So Easy, and S.L. Magic. Also, there's Kimi ni Shittochuu, Appletachi, and, surprisingly, Pride. Although Pride was an A-side, and an amazing single altogether, they don't play it much,.
Basically, I think that the majority of their B-sides are underrated, unless their used for promotion purposes. But a few album songs haven't been played as well, such as Hitotsu Dake, Glamorous You, and Sono Toki. But this is my opinion, and while some songs may be played live at the important venues, I feel that these songs, and a few others, are overlooked.