Nice work on this, sorry for taking so long to review it.

Note that this only fixes part of #437, though. It's still possible to get callback functions called during lua_close/GC, which can still lead to problems. For example:

local uv = require('luv')

uv.fs_opendir('.', function()
  print("opendir cb called")
end)

-- note: calling uv.run() would fix this example

will result in (with a printf added to loop_gc):

loop_gc
opendir cb called

During that callback, it could attempt to use something that has been garbage collected (and potentially freed) so there's a high chance of errors/crashes/UB/etc.

For example, this will segfault/UAF for me on Linux because it will free the pipe and then try to read its memory in the opendir callback:

local uv = require('luv')

local pipe = uv.new_pipe(false)

uv.fs_opendir('.', function()
  print("opendir cb called")
  print(pipe)
end)

-- note: calling uv.run() would fix this example

with some more debug prints added:

handle_gc: 0x4bae640
loop_gc
handle_free: 0x4bae640
opendir cb called
==12330== Invalid read of size 8
==12330==    at 0x4F994F0: luv_check_handle.constprop.0 (handle.c:56)
==12330==    at 0x4F9973C: luv_handle_tostring (handle.c:65)

But this is a separate problem to the one solved in this PR, so it doesn't need to block this being merged.

Note: I've edited the OP to make sure this doesn't close #437.