Distinct query in mongo with condition works like this
db.Article.distinct("Comment.Reply.ip",{"Comment.Reply.email" : "xxx"})
not other way around
EDIT:
I understand the problem now, inorder to match/filter subdocuments we need to use $elemMatch operator, like this
db.Article.distinct("Comment.Reply.ip",{Comment: {$elemMatch: {"Reply.email" : "xxx"}}})
but this will not work if the sub-document contains sub arrays (in your case, you have array of replies). There is an existing issue $elemMatch on subArray is opened. And its planned for mongo 2.1. You can check out the link for more info