Several times I’ve had the treat of hearing a band’s album, thinking of the first track “gee, that would sound great as their opening song, too!” and actually hearing it that way in concert!
This thread is not about those tracks. What (otherwise good)songs open up an album but would make bad concert openers? Note, I have never actually seen these as an opening song live:
Endemoniada - Fields of the Nephilim. Sure, the 7 minute long prog-metal song has a great buildup but would it be that great to just sit around for the first 5 minutes hearing frogs croaking rather than the Goth Metal we came there for (an exaggeration of course.)
My Paper Heart - All-American Rejects. If just for the fact that it’s their best song and I wouldn’t want them to blow their wad right away 
Shine on You Crazy Diamond - Pink Floyd. See first entry.
As a corollary, there are some songs that open albums that simply shouldn’t be. The first song on an album should be punchy and uptempo, not some bleepin’ dirge.
The best example I can think of at the moment is Outside World leading off Midnight Oil’s brilliant album, 10,9,8,7,6,5,4,3,2,1. It’s a good song and all, but it is a synth wank that never gets moving, even though it threatens to, (songus interruptus).
And I wouldn’t want them to open a show with it, either.
Genesis used Mama as the opening song on their Invisible Touch tour. I don’t think it was a particularly good choice. I like the song, but it takes a while to get going.
This (all 9 parts) was the show opener for the 1987 “Momentary Lapse of Reason” tour. This actually got the most crowd response in the first half of the show, as they proceeded to play nothing but new material until after the intermission.
The Band chose “Tears of Rage” as the opener for “Music from Big Pink” specifically because it was slow and dirge-like. Not a typical concert-opener, either.
“Closing Time” would have been a bad choice for Semisonic to open with.
I’ve never seen the band Garbage in concert but every time I cue up their first album and “Super Vixen” starts off, I think “It sounds like they’re having a sound system malfunction”