Why does agrose gel runs horizontally, and SDS-PAGE gel runs vertically?
When you stand general agarose gel vertically, the gel is slippery coming out from the bottom; although, some run vertically. 

To polymerize acrylamide, it is good idea to avoid air because oxygen inhibits polymerization of acrylamide. You would get an air tight condition, pouring acrylamide between glass plates, but how could you run gel made between glass plates. When you set such gel plates horizontally, how do you load samples? Then, it is easier to set gel plates vertically.