Summary
('Alphys' parts A, B, and C, as heard in Alphys)
'Alphys' is the theme of Alphys, as heard in Here We Are, and, y'know, Alphys.
It also appears in two other songs:
She's Playing Piano
(the 'She' referring to Undyne, reflecting their relationship)
Bird That Carries You Over a Disproportionately Small Gap
(reflecting the similar nature of the characters in question: underconfident and yellow)