Which one is better and ideal in a web based application?
Edit:
Actually I am developing a community site. So the level of users may vary. Heard about XSS security issues with WYSIWYG editors. Also I am not familiar with WYSIWYM editors and its features. As far as I know the features in WYSIWYM editor is less compared to the other one. I figured one named as "WMD: The Wysiwym Markdown Editor". Its quite easy to use.
So security and ease of usability should be there. In such a situation which editor will be better.
Answer
If your users can handle WYSIWYM, I'd go with that.
I'm considering your system will be visual, that is, if you say something is a title it'll look like a title (otherwise the WYS part wouldn't apply). If the user has to manually type markup, then only the most savvy or technical users will be able to handle it.
What I've seen with most users is that they have trouble giving meaning to what they want in a document. They don't think "this is a title", they think "this should be bigger and bold". People that cannot think "this is a title" can't handle a WYSIWYM or they'll find it hard.
Who is going to be your user base? If it's people writing academic papers I'd go with WYSIWYM because they'll have no trouble handling it. If it's for house wives writing recipes, they may not be able to handle it or they'll find it so hard that they'll decide it's not worth the effort.
For me the ideal is WYSIWYM, but do it only if you think your target users will be able to handle it, otherwise you'll have to go with WYSIWYG.