Likewise, if you will be using a WYSIWYG editor module (such as FCKeditor or TinyMCE) with Filtered HTML, at a minimum add <p>, <br>, and <br /> to the default allowed tags list. This will make sure line breaks and paragraphs entered in the WYSIWYG interface are not stripped out by Filtered HTML.
In either case, but especially if using a WYSIWYG editor module, consider expanding the allowed tags even further. For example:
<a> <p> <br /> <br> <blockquote> <div> <span> <address> <cite> <quote> <code> <pre> <em> <strong> <sub> <sup> <h3> <h4> <h5> <h6> <hr> <ol> <ul> <li> <dl> <dt> <dd> <table> <td> <tr> <caption> <img>
(WYSIWYG editors may also make use of <b> <i> <u> <strike> tags in their own markup, and so these should be added unless other solutions are implemented.)