I'd have to agree with what wrldstrman says. Here's my list:
Best of the Best - I don't think I've ever seen the box for this game
Chubby Cherub - We all missed
THIS auction. That makes 2 in the past 8 months.
Jimmy Connor's Tennis - Sosafan2 and myself have one on ebay for sale right now (even though I really don't want to sell it; I think my price is high and use it as an attraction)
Challenge of the Dragon - Only seen a handful of these boxes
Sachen games - Well, Sachen games themselves are hard to find let alone their boxes/manuals.
Sqoon -
THIS auction ended just the other day complete
Mickey's Adventure in Numberland - I think I've only seen it complete twice....
Secret Scout
Sunday Funday - Until recently when billmarioman got a hold of a bunch of the boxes and has been selling them on ebay. The cart is still extremely hard to find though.
Pro Sport Hockey - I think this is harder to find than Jimmy Connor's Tennis. Even though one just sold recently on ebay....
And probably the hardest PAL game to find complete (not Rodland):
SMB/Tetris/NW Cup - I didn't even know this game came with a box until someone over at DP showed one for it.
Those are the ones I can think of right now. I might have to change it later. But I really wouldn't say Menace Beach and Bonk's Adventure would be in this catagory because if they show up complete on Ebay then they most likely go more than that.