We allow Make Whole to apply to magical items on the off chance someone wants to sunder some things. Our next campaign also uses a different way to generate treasure, so it's not a punishment to the PCs.
On the whole, though, it's a niche ability, depending in large part on the setting. In standard D&D, though, you're usually fighting monsters, so JaronK's points apply. I was once upon a time playing in a campaign set during the Crusades, and there sundering was a relatively useful tactic.
We're also trying out some house-ruled versions of all the combat maneuver type feats to try and see them get more play. Just like disarming, I could see if it's only a 1 feat investment and something that is reasonably useful to use in some cases -- e.g., sunder the Antipaladin's black sword of doom(tm) -- I could see people using it. I think I'm taking it for flavor reasons w/ my Mo9, and fighting guys w/ swords will be relatively frequent in the setting, so I'll let you know.