I know what is easily the most intense "duo bosses" experience that I've had, and that's the back-to-back Satans from Ghosts and Goblins on the NES.
The reason, of course, is that if you've reached them, you've somehow managed to get through one of the hardest levels in all of gaming and also go back, get the shield, and climb up to these two Satans with enough time left on the clock to fight them. Assuming you do this, you then have to kill both Satans back to back (with the odds being fairly high that you'll be in a one-hit-and-you're-dead scenario), and if you fail then you're sent back to the beginning of the level with the damn shield, which is useless for most of the enemies of that level (as in you'll have to farm for another weapon again).
They may not be the coolest bosses, but they've always been the most memorable to me as you're so damn desperate at that point to get through them. The following final boss (The Devil) is a cakewalk next to those two.
