Yogg, Sinestra, Ra-den
Seeing the questline to unlock Algalon back in the day didn't require you to kill Yogg-Saron I don't find Algalon to be the last boss in any way of Ulduar.
Sinestra did feel like the last boss since she's at the very end.
Ra-den is a little 50/50. I feel he's the last boss cuz he should probably be dealt with and he's not available until you beat Lei Shen. However, I also wonder what's the big deal if we didn't kill him...
Algalon would've sent the code to re-originate Azeroth, bad.
Sinestra would probably make more dragons, bad.
But what would Ra-den do?
Guess he'd destroy the world from the sounds of it, but I don't feel quite as intimidated by him as I did Sinestra/Algalon. He just seems a bit crazy and seeing how he's been imprisoned I don't feel that worried about his powers, unlike a scary giant dragon or this mysterious observer guy. In the end I think of him as the final boss since he's only available at the end. But just barely I think...