I would definitely go with the wikiEntry.Comments.Add(newComment) method. I've listed my reasons below.
It feels intuitive because it is the same way Microsoft's existing controls work, so your code naturally feels like a part of the codebase.
It separates functionality of one thing - Comments - into its own area of responsibilities. Within the Comments collection you can add, edit, remove, order, etc. That way you don't cloud the main namespace if, say, you wanted to also be able to add, edit, remove, order, etc a list of References, Editors, Moderators, historical snapshots, whatever (not saying you would want a collection for each of these, many/most you probably wouldn't)
You can reuse the Comments collection in other classes and already have functionality built in for handling modifications to the list.
Think: wikiEntry.Comments[parentComment].Comments.Add(newComment);
gives you an easy way to represent nested comments.