It grated on me when journalists called it "Nee-jer" during the Joe Wilson story, they were wrong. Same with calling Qatar "cutter". I couldn't believe how stupid they were.
That's because that is the proper pronunciation: /niːˈʒɛə(ɹ)/, altho /ˈnaɪdʒə(ɹ)/ is also acceptable. The former is what you get when you apply French phonetics to the spelling, the latter is what you get when you apply English phonetics. Since French is the offical language there, applying the French pronuciation makes sense. Qatar sufferes from the fact that English and Arabic use different phonemes and of the phonemes in the Arabic pronunciation, /ˈqɑ̱.tˁɑ̱r/, only the r is in use in English. So depending on which way you shade the phonemes to an English equivalent, you end up with a lot of different pronunciations.
I guess thats why the city of Benghazi has like 6 different ways of being spelled. Arabic is a tricky language.
Actually, the problem lies not with Arabic but with Latin spelling - its' characters are used to represent so many different things in so many different languages by now it's just not funny anymore, and it's number of characters is actually rather limited - which is an advantage in learning to read and write as kids, of course, but for expert phonetics it's useless.