The Flaming Lips - Embryonic. Developed and sequenced as both a double C D and L P, but more widely made available as a single C D, since the two halves fit on a single disc.
Oneida - Rated O. Both a triple C D and L P, so no surprises if listening to the L P version.
Excepter - Presidence. Two C D's, no L P version. If there had been, two of the tracks, 'Presidence' and 'Og', would have been split into two sides, as they're both around a half-hour long; in general, the album's a mess by their standards; the tracks collectively titled 'Teleportation', also totaling around a half hour, would've made for an excellent single L P; another L P could've consisted of 'The Open Well' on one side with 'Leng' and 'The Anti-Noah' on another.
Joanna Newsom - Have One on Me. Triple C D and L P, same set-up as Rated O--the C D's aren't long enough to cause sequencing problems for the L P's.
Kate Bush - 50 Words for Snow. Single C D, double L P; side A's too long and B's too short, but overall it's sequence of tracks works well in both formats.
Lou Reed/ Metallica - Lulu. Double C D and double L P; sequence works fine for both formats.
Swans - The Seer. Different sequence of tracks for the triple L P and the double C D. The Discogs entries give you the lowdown.
Scott Walker - Bish Bosch. Single C D and double L P. Sequence fits L P version perfectly.
Neil Young - Psychedelic Pill. Double C D and five-sided "sesquialbum" [see below], same sequence.
The Invisible Hands - The Invisible Hands. Double L P, the same songs by Alan Bishop, formerly of Sun City Girls, recorded twice with a Cairo-based band, once in English, once in Arabic. C D version only contains English-language versions.
The Knife - Shaking the Habitual. Double C D and triple L P, same sequence; the L P sides are awfully short--a good example of not ruining the sound quality of the L P with narrow grooves [see below].
Since the C D supplanted the cassette and L P around 1990, albums have generally been too long. A positive side effect, though, is that those artists who give more thought to issues of sequencing, and have understood the need to avoid unnecessarily-long albums, challenge themselves by making more double and triple L P's. Then again, artists realizing they have on their hands an album that works best being 50-60 minutes long can accept an impractical, but audiophile, solution: refuse to stretch the length of L P sides, instead putting out a short double L P or a 3-sided L P.
Sonic Youth - Dirty
Frank Black - Teenager of the Year
The Verve - A Northern Soul
Radiohead - O K Computer
The Flaming Lips - Soft Bulletin
Bob Dylan - "Love and Theft"
The Knife - Silent Shout
Panda Bear - Person Pitch
Animal Collective - Feels; Strawberry Jam; Merriweather Post Pavilion
Taking a broader historical perspective now, some 3-sided L P's (besides both of the Angels of Darkness, Demons of Light albums)--and no, this category doesn't include L P's with a bonus seven-inch, such as Pavement's Crooked Rain, Crooked Rain, or double L P's with such, like Stevie Wonder's Songs in the Key of Life):
Johnny Winter - Second Winter
Keith Jarrett - Eye of the Heart
Joe Jackson - Big World
Julian Cope - Jehovahkill
Thurston Moore - Psychic Hearts
Pavement - Wowee Zowee
Built to Spill - Perfect From Now On
Of Montreal - The Sunlandic Twins (third side referred to as an E P, but it is not: an E P would have the five tracks spread across two 45-R P M sides, instead of all five on a single 33-and-1/3-R P M side)
The Wikipedia section on sesquialbums notes the Norwegian band Motorpsycho, the true stars in this realm with two three-sided L P's and one five-sided. Besides Neil Young (noted above), The Mars Volta also have a five-sided album, Frances the Mute.