incompatibilities

behavior

= to a variable declares it on the current scope. Use := to modify ones on upper scopes.
===/!==/==/!= each compiles as is.
super represents the direct reference to the parent function rather than being a call itself. Use super ... (just super in Coffee) for full delegation.
Nested comprehensions return flattened results.
Within non-triple-quoted strings (''/""), indentations after newlines are ignored altogether.
do does not specialcase function literals. Use let instead.

The roles of in and of have been swapped to keep the JS semantics.
yes/no/on/off are unreserved. Define your own or just use true/false.
switch-case-default replaces switch-when-else.
for ever replaces loop.
is not replaces isnt.
void replaces undefined.
~> (wavy arrow) replaces => (fat arrow).
when is removed. Use a if b while c instead of a while c when b.
it/that/fallthrough are semi-reserved. They get special meanings depending on context.
eval/arguments are keywords as per ES5.

() is always a call; allowing f (), disallowing () ->.
... is prefix as per harmony:spread.
and/or and spaced ./?. close implicit calls. f a .g b or h c means f(a).g(b) || h(c).
The range syntax (x..y) is removed.
Block comment is /* */ rather than ### ###.
Heregex is // // rather than /// ///.
No implicit call against blocks starting with an impilcit object. (Use do instead).