Go for it! Do not hesitate to use those nifty javascript popup menu's!
But there is a trick that will help you with Bots traversing your website...
Place all of that bloated text links that you have at the bottom of your pages with a hidden <div> tag right at the top! Just put your text nav inside a hidden <div> right after your <body> tag.
Here is an example website to view the application of this little trick:
http://www.kroc.com/kroc_fm/
And here is an example of how to implement this little trick:
<div name="navigation" id="navigation" style="visibility:hidden; height:1; overflow:hidden; background-color:#000000" class="font_microscopic">
NORMAL TEXT LINKS HERE
</div>
That's all there is to it!
Also, check out this site for all kinds of great info on youyr robot instructions:
http://www.robotstxt.org
Hope this helps!!!