I use 60 when playing Shogun. this allows for more manuevering, as the maps in STW are smaller than in MTW (and, I assume, in RTW). Morale (and hence, flanking) is "the name of the game" in TW battles, so manueverability on the map is tres important.

I've played some interesting multiplayer MTW games with 100 men per unit. The battles last longer, and ranged units (archers in particular, for obvious reasons) seem more effective. Because the maps are bigger, I didn't feel that my cav units' mobility were limited.

The main problem with larger units is it can cause a lot of lag when playing online if even one player has a slow connection or PC. I was using a very old PC over a dial-up connection when I was active, so I preferred 60-man unit sizes in STW, and the default unit size in MTW.