Minecraft – way to prevent animals from escaping a fenced area

Since version 1.5, this hasn't been much of an issue, as that release introduced a rule in the mobs' AI to avoid rails unless they are chasing after the player. Although I have still found Zombie Pigmen appearing on the tracks, this is now not as much of an issue as it was in previous versions.

Zombie Pigmen are able to spawn on rail tracks, so removing the walking path on the side will do nothing. But as has been mentioned, adding blocks above your tracks will prevent them from spawning and help keep them from walking onto your tracks 100% of the time. This is a common "fix", and has been around for quite a while, and it doesn't seem like the developers have any plans to stop this fix from being possible.

The following blocks can safely be placed above the tracks, and will not suffocate you:

• Glass panes (I would really recommend this one, since they are "cheaper" than glass blocks, works with stained glass panes as well)
• Glass blocks (works with stained glass as well)
• Glowstone blocks
• Leaf blocks
• Iron bars
• Fences (of all materials)
• Half-slabs (of all materials, note that they must be single, NOT double slabs)
• Stairs (of all materials)
• Trap doors
• Pistons (both extended and retracted)

There are other blocks that would work, such as Beds, Chests, TNT, or Enchantment Tables, but I have excluded them from the list due to being impractical.

If you watch at about 2:50, you can see most of the left half of the circuit. The part for the stairs looks like it isn't shown very well but that is less important timing wise. Watch carefully over and over and see if you can replicate it this way. It looks like the repeaters for the middle activate and deactivate immediately. So the order (from a circuit standpoint) for both directions is M, L+R. This works for closing because the middle repeaters don't have anything to activate until the blocks are pushed into the middle. When opening, they will retract the middle immediately.

Breaking it down:

Opening

1. Middle repeaters deactivate (middle pistons retract)
2. Delay
3. Left and Right redstones deactivate (left and right pistons retract)

Closing

1. Middle repeaters activate (nothing happens because the middle pistons are not in position)
2. Delay
3. Left and Right redstones activate (left and right pistons extend)
4. Now the middle pistons have been pushed into position and are activated by the middle repeaters