13th Floor Elevators - Fire Engine and Slip Inside This House are different edits + many of the 45s are different mixes aswell. Most notably Levitation if I remembr correctly
Another one that springs to mind is 20th Century Zoo - Rainbow. Totally different edit and mix than one the LP. Way more punkish.
The Monkees - Porpoise Song has different mix, and the freak out ending that's not on the LP. The freaky ending is added on the old Rhino reissue though
Them - Square Room - both 45 versions are different. Ruff is a different recording and Tower is a different mix and edit (of course, as the LP version is something like 19867 minutes long) No flute solos on the 45 :)
The first press of MC5 - Kick Out The Jams (MC5-1/2) is a completely different mix and edit. No audience noise, louder guitars, pitched faster and a different ending. They tried to mix a 'studio version'. IMO it's much better than the regular version.
The Morgen 45 is different from the LP aswell
The Stooges 2nd 45 has "radio friendly" edits i.e. shorter and tighter, with shorter guitar leads etc. To good effect IMO.
But the most bizarre example, as far as I know at least, must be The Bougalieu - Let's Do Wrong. The stock copies and promo compies has completely different takes/edits of the same songs(!?) Does anyone know the background to this?