I pretty much use a specific system. For medium and short dungeons there is one savepoint at the end. If there is a boss, the savepoint is right before the boss. For larger dungeons USUALLY there are two savepoints. One is just like for the smaller dungeons, another one is at another specific point.
Reeva Cave: small, before the boss
Forest of Illusions: rather small, before the boss
Giada Castle (including Echo Cave): rather large, one at the entrance of the castle, the other before the boss
Great Marsh: medium, before the boss
Lorence Cave: very small (2 maps), no savepoint
Lorence Castle: medium, one before boss, another at optional boss (I wouldn't have set this one up if there was no optional boss)
Krato Mine: medium, no savepoint because you can return to Vendetta
Krato Mountains: medium, before the boss
Ghost Ship: very small (4 maps), no save point
Adel Tower: medium, outside of the tower, before the boss
Katana Desert: small, in the center at the oasis
Ice Temple (including Silent Forest and Ice Cavern): large, after Silent Forest, during 4-switch puzzle in the center, before the boss
Tower of Memories: small-medium (will be medium or medium-large later), before the boss
Cravgon: medium-large, at the entry / before the boss, you can always return to the savepoint, it's 3 maps from the center map where you walk around often
Molasta Pass: medium, before the boss
Termina Sewers: medium, at entry / before the boss
Ember Volcano: large, before the boss (I agree, another savepoint here might not be such a bad idea)
Andras Temple: large, before the boss (maybe another savepoint on top might not be such a bad idea here as well)
Mandora Dungeons: medium, no battles, still at entry
Mountains of Slumber: medium, before the boss
Crios (Island + Depths): large, one at transition between Island and Depths and before the boss
Genesis Dome: large, one at the top where a nasty puzzle is (halfway) and one before the boss
Unitopia Underground 1: small-medium, at the beginning
Luvia Underground: medium, no save point as I didn't want players to get stuck while being too weak
Thirsty Dunes: medium, one right before a nasty/dangerous puzzle and one before the boss
Unitopia Underground 2: medium, one at the beginning and one before the boss
Hyperion: gigantic, 5 save points scattered throughout the entire ship, one at each deck covering all bosses and two in between
I should probably add another one in Ember Volcano and in Andras Temple.
And maybe I'll add one when you start the game. But it would be kinda awkward because I'll maybe have to restructure some maps (again). :/ I'll think about it.