I too am considering both of these GPS apps. This forum has a fair amount of information, you should use the search.
After all the reading I have done I am leaning towards getting Navigon, simply because I really like the MyRegion option, $30 is easier to swallow than $60+. One of my main concerns though is if I start with MyRegion Central and then 'in-app purchase' MyRegion East at a later date does it download and install another application or does the current MyRegion Central application allow the newly purchased maps to become available? If it does in fact create a new application will the user be able to start in the Central region and cross into the East region? I haven't found answers to these questions on the forum, and Navigon customer service hasn't responded to my query yet.
Both the Navigon and TomTom store the entire map on the iphone itself. I think as of the most recent updates both also use Google Live Search for finding more points of interest. Both have ipod controls but everything I have read said the Navigon has better ipod controls. I also think both have lane assist and text to speech. Navigon has some thing called "Realty Vision" or something, where it will show interstate interchanges, and where you need to be during said interchanges. I'm not sure if TomTom has this. That's all I can remember off the top of my head.