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.
Unless you are doing a tool for print layout (i.e. Indesign or maybe a mailing list printing tool) you are probably better to stick with WYSIWYM.
It is likely to be easier to implement
Web browsers are highly configurable and you may not have fine grained control over items like font size.
The structure is explicit so rendering to different media is comparatively easy.
It avoids the temptation on the part of users to over-design the document or whatever they are entering.
Document structure facilitates indexing, table-of-contents generation and cross-referencing where this is relevant. Compare (for example) maintianing a large index in Word with doing in LaTeX or Framemaker.
Anecdotal experience from LaTeX users (in particular) suggests that organising a document by structure is likely to produce a better document.