I've got a small sample size of experiences, but I had zero issue with Brussels Air and Air Canada, and I'm using the box method again this summer. As far as I could tell, they were not mishandled, no unusual marks or holes in boxes, nothing broken or having shifted around in the box. The outbound leg they were carefully packed in LBS boxes in a manner they couldn't move, and the way back they were more or less rolled into oversize Amsterdam boxes with both wheels and all bolts on still on. When we got stuck behind everyone disembarking from two Mid East jumbos that arrived ahead of us us, and didn't get to baggage claim til over an hour later, we found the baggage folks had actually moved our bikes to a room for safe keeping. As with any traveling, though, you are always at the mercy of the individual baggage handlers.

DO give yourself time to make sure the boxes you get or build actually fit your bike, though, or you'll end up trying to "reengineer" the box at midnight the day before departure because your seat tube is a bit too tall to fit in the box (see the middle of the back box)



Quick tip I learned: those $1 foam pool noodles (hollow ones) make great protection for your bike's tubes when cut open and wrapped around. Also good to mark which end of the box is the back tire, because you may have to stand it up on end to get it through various airport barricades.