The best way to handle fractions that I've found is to illustrate them as what they are: parts of a whole. Pie Charts and fraction strips (proportional length cut outs) are the best manipulatives I've known. The strips are most useful at illustrating equivalent fractions, how to use them to find common denominators. The pie charts are particularly good for illustrating mixed numbers and improper fractions.
Another interesting way to illustrate them is musically. The Time signature of music is a type of fraction. The top number tells how many beats are in the measure, just like the numerator tells how many pieces you have. The bottom number tells what size note counts as one beat, just like the numerator tells how many pieces make up one whole.