Could you be a bit more specific? What kind of web application? How many users? Who will the users be?
In general though I've had quite of bit of experience implementing WYSIWYG editors for various CMSs and found them to be quite problematic because clients often like to go wild with formatting their content repeatedly over and over again and often end up having the editor generate HTML of poor quality. This causes all sorts of layout issues or simply pages that look really messy because everyone likes to fancy themselves as graphic designers.
If done properly WYSIWYG can work very well, but it is more work to really get it right, especially when taking into consideration CSS. Most of the good editors are nicely configurable and allow to specify just how much control to give the client over visual formatting.
As for the quality of the code they generate, tools such as FCKEditor and TinyMCE are very mature and do a good job of editing out the irrelevant crud in the source code, but be prepared to provide support for clients using a WYSIWYG when their content doesn't look the way they would like it to.
Since WYSIWYM editors are much like WYSIWYG with structural formatting instead of visual formatting, philosophically I think they are better and less problem prone. So if the client doesn't have a need to visually format the content I think WYSIWYM is bound to cause less headaches down the road.
The editor used here in Stack Overflow is a good example of restrained WYSIWYG. You can format the content visually but only to a certain extent.