@JeffZero - Yeah, basically what Audley said. It's supposed to be about the journey toward transcendence, I guess. The first half deals with earthly baggage, and then moves (with the song Lateralus) into a more metaphysical space. And, of course, there are the crazy Tool conspiracy theorists that insist the actual track order is incorrect for achieving that story, and thus rearrange it so it "makes more sense."
In any case, I think it's probably their most unified album in tone and feel, so in that regard, I'd consider it at least a loose concept album, and not just a bunch of songs with some transitional filler, like Aenima and 10,000 Days are.
Most of my favorites have already been named. Ziggy Stardust, Berlin, Thick as a Brick (does that count? It's not a collection of songs, after all, just one that's very long), Skylarking. Aimee Mann's The Forgotten Arm and Rickie Lee Jones's The Sermon On Exposition Boulevard come to mind, and as a long-time Kinks fan I should mention their Kinks Part One: Lola Versus Powerman and the Moneygoround, if only to divert everybody's attention from certain other concept albums i wish they hadn't made.
Actually, Thick as a Brick is particularly interesting. It's all the things I hate about seventies' rock (and concept albums, usually), but somehow they manage to pull it off in a way that's more engaging than aggravating. For me, anyway.
Dream Theater's Scenes from a Memory is my all-time favorite album. Maybe it just caught me at the right time, being an impressionably young musician, but I can't help but smile like a goon when that album plays.
Somebody already mentioned Ziltoid the Omniscient, but that album is truly a masterpiece. I would give anything HevyDevy to assemble an outfit to play that live. I mean it's a concept album about alien invasions, planet-smashers, puppets and puppets - what's not to love.
On a more stripped-down level is Defeater's "Travels" - although I'm not really into the hardcore scene, these guys balance the straight-ahead attack with enough catchy hooks and compelling lyrics to make me drop my jaw.
@taphead Promenade by The Divine Comedy is also a concept album...one day with an old girlfriend. I love it...you can't go wrong with sea shanties and songs listing famous authors. Blatantly rips off Michael Nyman and Scott Walker.
I always loved this album because it took a concept (Greatest Hits Albums) and totally flipped it. This album actually doesn't have any of his "Greatest Hits" and is instead complied of all new songs (not a b-side album or anything like that but is a full proper new release). It is also in it's own little way Phil Och's own life distilled into a single album. It details his boyhood (Boy in Ohio) and mentions his idols (Elvis, James Dean, etc) and the album ends with "No More Songs" which always sends shivers down my whole body.
Ah well, as long as I mentioned World/Inferno's Peter Lorre album, I may as well suggest 'The True Story Of The Bridgewater Astral League' as well. W/IFS's album about a gang of teenagers who steal cars and commit crimes in their sleep via astral projection.