If your menus aren't appearing in front of flash objects, then you need to look at the z-index of the menu items or menu container. It's a css element that would be placed in your skin.css file or portal.css setting the class assigned to the menu to have a z-index of 1000 like ".menuClass { z-index: 1000; } " That's one solution.
You could look at a third party menu called NavXP that is available on Snowcovered. It works similar to DNN360's Navigation Suite, but takes things one step further in allowing you to create custome menu "profiles" that can include "arbitrary" menu items (meaning you can add a menu item that is simply a link to a url without having to add a page in DNN to accomodate the link). It's a bit more complex in terms of learning curve, but I've been using it on a project and absolutely love it.
Another option is to use the core DNN HTML/TEXT module and place the menu on the page by editing the module in html view mode. You'd be hard-coding the menu, but be able to edit the menu without editing the skin.
Another option is to use Open Web Studio (OWS) from the r2i guys. It's a free open-source module for creating custom modules in DNN. It has a tremendous number of functions including the ability to create drop-down select boxes that are database driven. You'd be able to place a drop-down box on the page that is populated from DNN's core sql portal tables. I've actually done something similar on my own website http://www.dnnstyle.com. On the home page, the list of demo sites is generated by OWS. I do have a bit more complex setup that added a custom table so that I could have a checkbox to select which portals I wanted to display in the list that way I can keep a demo site I'm working on somewhat private before it's officially open to the public. OWS has a bit of a learning curve, but you can do just about anything with it. Their user forums have numerous examples of sql populated drop down select boxes as well as the thousands of other things you can do with it. The learning curve is worth it, and it does have a auto-generated template to get you started with a simple setup. Everyone doing anything Dotnetnuke should review the Open Web Studio module for DNN! If you'd like me to set up the module for you with a custom setup for your needs, let me know and I can be available for you at a very reasonable price.
Those are my ideas for you, hopefully one is of use.