Answer: This is up to the DM and they should consider the party's intentions with the stuff. Various books provide an inconclusive answer due to inconsistent descriptions of the Styx and the ontology on if water stops being a river if it leaves the river.
Fiendish Codex II: Tyrants of the Nine Hells says the following (p.39):
Any living mortal who comes into contact with the Styx must make a successful DC 25 Fortitude saving throw or be afflicted with temporary amnesia. The DC increases to 30 if more than half the character’s body is immersed, and to 35 for full immersion. The amnesia lasts for 3d6 days.
The Manual of the Planes says this (p.86):
The River Styx: This river bubbles with grease, foul flotsam, and putrid remains of battles along its banks. Those who taste or touch its water must make a Fortitude saving throw (DC 17) or suffer total amnesia. Treat the victim as if feebleminded (as the feeblemind spell). Even those who make their saves lose all memory of the events of the last 8 hours. Prepared spells remain in memory, although the victim might not realize they’re prepared.
In both cases, emphasis mine.
The first says those who touch the river, while the latter says its water. Fiendish Codex I says "The waters of the Styx". This means that there are three different descriptions of the same body of water.
And that's where we hit a snag. Take a bottle, go to a nearby river and scoop it full of water. What's in the bottle? A river? Water? Riverwater? Depending on your interpretation it can be any three of them. This is a philosophical point that the rulebooks do not answer.
A look per case, can you scoop water from the Styx and have it retain its properties according to the description of:
- Fiendish Codex I: Can go either way, depending on your interpretation of "The waters of the Styx.".
- Fiendish Codex II: No, because it specifies touching the Styx and not its water.
- Manual of the Planes: Can go either way, but leans towards a Yes.
So we have a Yes, a No and a neutral answer, meaning the score's a tie.
Conclusion: It is up to the DM. Determine a yes/no depending on how likely the party will try and abuse it. In case they do, deploy max hit die fiendish giant octopi.
If you do go with using the water, make sure to not touch the bottle as you take it out. Make sure to dry it off and NOT TOUCH whatever you do that with, lest you suffer the effects anyway.
Or cast a Maximized (and maybe Extended too) Hoard Gullet on yourself when you're at least level 10 (Dragon Magic, p.68) and find a way to fit 680 liters of the Styx into your mouth (note: only works if water from the Styx is the same mass and density as regular water), allowing you to haul around 1500 pounds of water which you can expel from your body into your square as a full-round action (bring protection). Then fly over some people you dislike and drop it on their heads. Serves them right.