If you are referring to the 1 piece adaptors with 2-plugs on them, then I would say stick to patch cables. I used to use those things, but what I noticed was when you step on one pedal, it makes the others around them move as well, and it seems to put a lot of pressure in/out jacks of the pedal. Plus if you are not using all Boss pedals (and even if you are) the in & out jacks of other pedals may not line up exactly, and you'll either need to shim up pedals, or have uneven pedal positioning. Then if you ever get a pedal that has its in/outs somewhere other than the sides, you'll need to get a patch cord anyways...so I'd say just stick with pacth cords.
I've always made my own cables, and because I have other pedals in the mix besides Boss the cables tend to vary in length anyway, so even the short connection between a pair of Boss pedals will be a couple of right-angle plugs and a short length of cable between them. Jack pretty much nailed all of the good reasons to go this route.