Don't know about Kobo, but the Sony's use collections (kind of like a playlist) which works good for organizing. The Opus has full folders which work great.
The Opus doesn't support bookmarks (it remembers where you last read, but you can't mark multiple pages) or multi level tables of contents if that makes a difference. AFAIK the Sony's use a slightly older ePub software and doesn't have the justification support the Opus does.
I personally don't like the center page turn button on the Sony 300 and prefer the side buttons on the Opus (the accelerometer lets you turn the device to re-orient the buttons). That's a personal preference thing though.
Can't really go wrong with either Sony or with the Opus.
You don't say where you are, but if you're in the US, Canada, the UK you should be able to find the Sony's in store to give them a try (not sure about other countries).