For me it depends on the situation entirely. Generally spearmen make a good target because Muslim armies are so cav-heavy. However, especially against Catholics, I love to run my HA behind the whole enemy line and harrass their most valuable units. The last battle I played I had two full 40-man HA units and one previously hurt 14-man unit. I took all three behind the enemy's (English) line, and I used one 40-man unit to specifically hit all their billmen. I used the other 40-man unit to run up and down just hitting and harrassing various units, killing 3 or 4 men in each. My favorite part was using the 14-man unit from about 10 feet behind the enemy's royal knight general. I killed 2 royal knights then dragged the general's unit all around the map while firing a couple arrows every now and then. They got so annoyed that they literally turned their whole army around to get rid of my HA. At this point I took my heavy cav and hit them in the rear to pretty much finish the battle. My infantry never even had to engage them other then to clean up a bit.

Point is, I generally use HA from the flanks or rear on their most valuable units. In particular, I find the units that I don't want to fight and try get them to follow me by shooting them in the back from very short range. They almost always do follow so I can proceed to destroy them with my other troops. Basically you can use them to tip the odds in your favor, even they aren't to begin with.