Stun, Daze and similar stuff don't impede your movement...
...they make your mind funny.
While you are stunned, there's nothing holding your body to move. You just can't think right to actually do something. If you take a really hard blow to your head, that won't make your body harder to move - it will make your brain go gonzo for a few secs, before you became aware of what's really happening.
Stun is not about movement, is about senses of what's going on.
Freedom of Movement makes "your body work right", not anything else. It allows you to move, but not allows you to think. You can't think if you're dead. Or Stunned.
Paralysis don't block purely mental actions, so it don't block "thinking".
Slow makes your body... well, slower, but it doesn't affect your thinking.
Web is... well, a web. It hinders your body, not your mind.
Stun, Daze, Dazzle and similar stuff, on the other hand, makes your senses go wacko, so they aren't really blocking your movement. Stun never stopped you from moving, it just stopped you from thinking for a while - and since you don't think, you don't act.
So, the point is,
If something affect your senses, Freedom of Movement can't help you.
Think like a "Houdini Effect". Houdini can escape from almost anything, considering that he
knows what's going on. If you throw him with a concussion inside a closed coffin... well... he will stay there.
So, to determine what Freedom of Movement removes or not, use a simple rule:
Why I can't move?
If you can't move because a spell or something is hindering your body to move, like Web, Freedom of Movement can help you.
If you can't move because a spell or something is making your brain go gonzo, like Stun, or because your body becomes something that can't normally move, like stone from Flesh to Stone*, it won't help you.
*Flesh to Stone don't impede your movement, it merely limits you to the movement that a stone statue is allowed to do. A "Freedom of Movement"-ed and "Web"-ed person would become a completely untangled stone statue.
Also, read Freedom, the 9th level spell:
The subject is freed from spells and effects that restrict its movement, including binding, entangle, grappling, imprisonment, maze, paralysis, petrification, pinning, sleep, slow, stunning, temporal stasis, and web. To free a creature from imprisonment or maze, you must know its name and background, and you must cast this spell at the spot where it was entombed or banished into the maze.
Emphasis mine.
Freedom removes a bunch of effects, like Flesh to Stone and Stun. It would seem rather... strange to say that a way lower-level spell can do almost all the things that a 9th level spell can. Freedom is Freedom, not Freedom of Movement.
Best Answer
The best link I've found is to Unearthed Arcana which talks about adjusting saves for massive damage. It should be possible to extend that system to insta-death saves for other things as well.
The only other solution I would recommend is to back-port some rules from 4e, where conditions worsen over multiple saves. While it isn't a formalized 3.5 thing, it was clearly introduced to combat the same problem. The typical progression is:
And works quite well for increasing the feeling of risk without risking insta-death by one bad roll.