I recall that Dive is required for most of the sea based dungeons, but I never risked loosing the HM, so I always had at least one Water Pokemon learn the move ahead of time. Same went with Waterfall. It was always easier to do that than to keep the item on hand when you had limited Toolbox space to work with.
Faraway Sea, I think. I'm not sure. I only just beat the game again and haven't gotten through the first post-game dungeon for Kyogre yet.
Mmm, I forgot where you can get the HM for Waterfall, but I know several of them were in Solar Cave. It's been a long time since I played through that level, though, I don't recall specifics.
Cool. I just beat my recent playthrough of PMD: Blue Rescue Team last night, now I'm trying to unlock all the extra dungeons and clear them before I get the BW2 games.