Well, I can tell you how I use javs in MTW. As I play with Hungarians, I have found them irreplacable for dealing with that damned katatank generals!

The tactic "from the book" is this:
The main body is a spearwall, of let's say 3-4 units of spears 5 ranks deep each. Behind them are 1-2 units of slav javelinmen 2 ranks deep. Behind javs are 2 units of archers and 1 crossbow unit 3 ranks deep each. On my flanks are men at arms and urban militia (for flanking of course). Further out on the flanks I put horse archers (or szekelys, even better!). My general royal knights are far behind so that they can flank on either side, as needed.
Stupid AI will charge its katatanks in the spearwall, and once it's pinned, one o two volleys from my javs and archers and xbow will decimate all those katatanks. Then I use urban militia to finish the armored units, men at arms kill any spears and horse archers flank the enemies rear guard and harrass the archers.
Of course, the tactic will never be the same, much depends on lay of the land and opposing units. As a general rule, put javs behind your spearwall.

Also they are pretty valuable for bridge defense. Yesterday I defended a bridge in swabia. I had mainly javs and archers and one spear and two urban militia. I've poisitioned them in a classic U shape with the center of fire on the exit point of the bridge. Stupid AI charged with everything they had (including archers) at the same time. Of course a bottleneck appeared. As soon as a unit (any unit, even general) stepped on my side of the river they started to rout thus creating panic for every unit that was crossing the bridge at the moment while they are trying to flee from the "rain of death". Body count: me - 20 men, ai - 1400 men.
Sweet!

I would recommend a unit or two in every army since they will break a stalemate in a second. Just for the love all you recognise as holy, don't let them shoot up the hill! They'll mown trough your own units instead. Oh, I almost forgot! Put them off skirmish AT ALL TIMES, or they'll never get to shoot.