I get all of them to run nicely here, maybe I can help ;)
What is the distribution you are trying to get these to run on?

Linux Mint 18.04 pretty sure.

Though sorta too late, already reset the other laptop with windows, not that i wanted to.

Well, for next time: ./play.it already as support for Fez and VVVVVV. And support for Shenzhen I/O is only waiting for feedback before it can be integrated: [./play.it] Install Shenzhen I/O on Linux

Linux Mint is part of our target distributions, like any Debian derivative, so it should run there with little to no tweaking required.

Those games weren't the problem, those three were the ones i had NO issues with. I tried (among other games):

BeatBuddy
Clarc
Little Inferno

Might have been a few more, but weren't GoG titles (Humble Bundle games) though not recognizing any others that i tried... (Oh hey, Hacknet and Pony Island are in my HB listings. Fun fun)

Right, reading failure on my side ;)

We have ./play.it support for at least some of these:

• BeatBuddy (humblebundle.com version)
• Little Inferno (gog.com version, but I could add support for the humblebundle.com one on request)
• Hacknet (gog.com version, I do not have access to the humblebundle.com one)
• Pony Island (humblebundle.com version)