And it’s not the one you’re thinking of. Mozilla, I pit thee! You have caused my bookmarks and preferences to vanish from the mortal coil, whilst leaving my history file intact. Now I am forced to reconstruct the dozens and dozens of links that have disappeared, like so much Ralph Macchio career.
Oh, you poor non-Opera users.
Just kidding, I’m sure Opera has its share of problems. Having never encountered any major ones, though, I can’t say for sure. 
I had the exact same thing happen to me. Apparently it’s a known bug. Well, unknown to me, but known to others. Real bummer.
Yikes, didn’t know about this one. I tend to export my bookmarks to a file and upload it to my Yahoo briefcase for backup, but haven’t in a while.
It’s no help now, but for the future try this extension:
http://extensionroom.mozdev.org/more-info/bookmarkbackup
It’s saved my ass on at least one occasion.
They laughed when I accused my browser, and I killed them; we’ll see if they’ll be laughing noooowwwww!!!
Seems like a pretty major bug to me. Is it fixed in the more recent versions?