[SSJup81]

Can't comment on "ぢ" or "づ", since I've seen it both ways and probably depends on what you're spelling, but as for を, it can be pronounced both ways.

First and foremost, を is used as an article. 手紙を書く. (Tegami o kaku). You can pronounce it there as "o". Also, if I'm not mistaken, usually when を is at the end of a sentence, you probably pronounce it as "wo".

Sorry if I'm being confusing, I can't really explain it, so I guess I'll just leave it up to the experts around here. ^^