Avoid "window" seats in rows 7 and 9 on the 734 and row 14 (I think) on the A333 as these are windowless. Also, on a few of the newer 744s (not to be confused with newly-reconfigured 744s), there are no windows on the starboard side for two rows located at the very back of the Y cabin (i.e. last two rows or in two of the last 4 rows?) - so despite having just two seats on the sides, some of these rows may lack windows. If you must get these two-seaters at the very back of the cabin, get the ones on the port side to ensure you get windows.
For your EWR-KUL vv legs, try to get seats in the first Y cabin, rows 28-37, as this part is much less bumpy than the cabins behind the wing. Also, this cabin section tends to be less noisy being located ahead of the engines' jetblast "area". You can call ahead to pre-reserve specific seats. It's a long flight, so you want to get comfortable.
Also, for the long haul flights, if you get peckish, they do offer sandwiches, snacks etc - do not be afraid to use the call button for prompt service. For the short hop to/from SIN, you'll get just a beverage (juice/ tea coffee) service in Y.
On the whole, you'll enjoy the flight. At times and in certain departments, MH can be better than SQ.