Boss style is my favorite.
I did a few 1590B top-mount builds, when I was trying to get the most pedals in the least space. But the inability to use pancake-style jacks was a big turnoff; and I also got a two-tier pedal board which allows me to nicely space everything out, making the whole side-vs-top jack thing moot anyway.
So now I'm defaulting to 125B top-mount, because that seems to be the most common enclosure assumption for retail PCBs (e.g. PedalPCB, Aion, etc).
However, one thing I don't like about top-mount 125B is that it generally adds a fair amount of implicit cable length. That is due to having the switching at the
bottom but the I/O jacks at the
top; so even in bypass mode your cable length is about 2x the length of the enclosure. Of course there are workarounds: I've seen a few builds here that use a dedicated bypass PCB that gets installed right up by the jacks. And for circuits I
really like, I'll design my own PCB with the switching (relay bypass) integrated onto the effect, right at the top to be close to the jacks. Also, with a well-placed buffer or two, it probably doesn't matter (but some of us obsess over these kinds of details!).