Honestly, I have used IE6 in a very long time but the issues you are seeing aren't necessarily related to mojoPortal as much as they are xhtml/css.
There is an IESpecific.css file in all of the included skins that will allow you to set CSS that will work correctly in IE6. If you are having problems with IE7, use the IE7Specific.css file. From what I have noticed, IE8 and FF display sites darn near the same.
There isn't a recommended browser for mojoPortal necessarily. I do recommend something a lot newer than IE6 for any web browsing. IE7 was released 3 years ago, it is time to upgrade. I understand that you may not have a choice there so you are probably going to have to use the IESpecific.css file to make IE6 play nice.
Out of curiosity, can you post a link to your site? I might be able to find the problematic elements or selectors.