Shuffling Cards into Library
Personally, I'd check for agreement with both the player and his opponent about what lands were shuffled in. If they both come to an agreement, then I would personally take those such lands out of the library and put them onto the battlefield, then have the player finish the shuffle. Remind him to be MUCH more careful when he shuffles.
Now, let's infer that they don't come to an agreement, or the opponent doesn't remember. In this situation, I would actually look at the game state (which is unusual) and see if there is a logical answer to the question. For instance, the player and the opponent both say that they've played a land down each turn, and, therefore, the player should have “x” more lands. The same could be said by looking at the mana costs and making the best decision possible given the information. For instance, the player has several cards with a mana cost of 1-4 on the field, but their hand has mana costs of all 5s (also considering that there are no cards such as High Tide or Dark Ritual in the graveyard). At this point, it would be a personal judgement call on which lands would make the “most sense,” and checking to see if both the player and the opponent would be/are satisfied by the fix.
While this kind of fix is by no means definitive in how it's resolved, it's the best we can do as judges to rectify the situation and, hopefully, make both the players happy so they can resume the game. I believe that the saying “deviate like hell” is the most fitting to this situation.
I hope my opinion helps some!
-Peter