Don't forget: The main reason "Happy Birthday" sounds "upbeat" and "Eleanor Rigby" sounds "doleful" is that their composers intended that they should. And because that's what their composers obviously intended, that's the way the songs are typically performed. But there's much more than tonality that goes into evoking those moods.
Take "Eleanor Rigby." It's actually a very bad example of the idea that minor key tonality is inherently sad. The best evidence for that view would be minor key songs that are stubbornly, ineffably sad despite other song elements—lyrics, arrangements, tempo, etc.—that are emotionally neutral or positive. The worst kind of song to adduce in support of minor key determinism is one in which any sadness intrinsic to the melody gets a lot of "help" from the other parts of the song. And "Eleanor Rigby," remember, was considered a breakthrough for the Beatles precisely because it was one of their first songs of this kind, one that combined song elements in mutually reinforcing ways to create a unified artistic whole.
The dank pall enshrouding the Beatles' original recording of the song depends on a musical context broader than simply its chord progression and melody: Bleakly atmospheric story-song lyrics, obviously, and more subtly, George Martin's production, especially the chilly, staccato strings, implacably clocking the flight of time with their tick-tocking rhythms.
Still think the song's emotional valence is largely reducible to its minor tonality? Try a thought experiment. Don't change a pitch in the song's melody—but imagine it performed by a good-timey band, say Madness or the Specials: Speed up the tempo, put a ska beat under it (amazing how this change alone can transform the vibe), add steel drums, lots of horns. Substitute some lyrics that convey an un-self-conscious, slightly libidinal joie de vivre. Have a chorus of exuberant male voices sing them in unison. I tried something like this. My substitute lyrics were too embarrassing to include here, but they proved their experimental worth: The reductive view that in music the minor third is inherently sad doesn't pass the Ska Rigby Test.
It doesn't look like the interval is inherently sad in speech either. I raised the question with Gideon Rosen, a Princeton philosophy professor (and the unofficial musical director of a band I once sang in called the Mystery Dates.) As he pointed out, "The schoolyard taunt—Nah, nah na-nah, nah—begins and ends with a minor third ... but it's not sad: it's sort of hostile."
Gideon's schoolyard speech example suggests another from music, the similar melody (probably no accident) from the chorus of a famous Queen anthem: "No time for losers/Cause we are the champions ... of the world." I count 3 minor thirds here: We are/champions/of the.
"Sad?" Hardly. Try "exultantly, boastfully jeering."
Another example just occurred to me as I sat strumming: Jonathan Richman's "Egyptian Reggae." Inspired by an earlier reggae song, this simple instrumental novelty is plain funny, and part of its humor seems to spring from the exotic, vaguely "Egyptian" associations its minor key melody mysteriously evokes in Western listeners. (It's even funnier if you suspect, as I do, that the source of the melody's "Middle Eastern" redolence lies in its resemblance to a ditty called "The Streets of Cairo, or the Poor Little Country Maid"—sometimes known as "The Snake Charmer Song"—composed by American entertainment impresario Sol Bloom for the popular Egyptian attraction at the World's Columbian Exposition in Chicago in 1893.)