A trick I use sometimes is to only add pencil marks by 2s...if a box, row, or column only has 2 squares that could be 4, for example, then I'll mark the 4. If there are 3 squares that could be 4, I don't mark it (yet...if it's a difficult puzzle, I'll go back and fill in all the pencil marks later).
Doing it by 2s means that pairs are really easy to spot.