For me it depends on the conditions.
If I am sitting at the front of the line at a red light, I will put it in gear and keep the clutch pressed. You don't want to keep people waiting after the light turns green. If I am second or third in line, but I can't see the light (because maybe I am behind a truck), I might keep it in gear as well.
If I am sitting more than a few cars back in the line at a red light, I will put the car in neutral and take my foot off the clutch. There will be plenty of time to see the light change and get it in gear before the cars in front of me start moving. The same goes for being second or third in line if I can see the light change.
If I am sitting first in line at a long light, but I can see the green and yellow lights facing the cross traffic, I might take it out of gear. When the crossing traffic light turns yellow, I have time to put it in gear before my light turns green.
Sitting with the car in gear with the clutch pressed isn't a good habit, but considering the minute amount of wear that occurs when you do it, it isn't a big enough problem to keep people waiting while you shift into gear. Just plan ahead when you can, and hold it in gear when you can't plan ahead.