what is rooting? Should I upgrade my Xperia U from GB to ICS?

I have an Xperia U[GB] and there are certain apps which do not work on it[device is not rooted shows up everytime I try to open these apps]. So what exactly does it mean by rooted device. Should I root my device? Does it have any negative implications? Also I still haven't updated it to ICS,since I've been told that Xperia U doesn't perform well with ICS.So should I upgrade it?