I can't really comment with any authority on this as I only collect for a couple of specific franchises. But I would say the best one for Mass Effect was the Italian exclusive Alliance edition of ME3, limited and numbered to 1100, though it didn't have anything that great inside, just the collectors edition, the SR2 Normandy replica and a notebook, but the box itself is really nice with some great artwork on the inside cover.
For MGS there are plenty, but are the rules for only PS3/360/PC? because the Konamistyle Portable Ops PSP package is really nice.
