Flash has a bad name in general for search engine optimisation. Sure, there are plenty of websites out there that are built with Flash, and that rank well. The problem here is that you often have to do the work twice - once in Flash, then again in HTML.

Search engines don't read images (Flash is a way of presenting images / video on a website) and require text to decide what your website is all about. And HTML is the king of text content on the block at the moment. Since Flash is essentially centered around a visual experience, whether it be video, or video and audio, this inherently makes it less search engine friendly.

A well search engine optimised website can be achieved using Flash - it's just not usually as cost effective when compared to a html/xhtml/css website. Of course, Flash has it's place - it is for good reason that it is usually the primary choice when designers want to add interactivity to a website in the form of audio/video. Keep your eyes peeled on the latest CSS offerings and specs though - we're seeing a lot of progress in terms of graphics, and soon possibly video too with standards compliant xhtml/css.

If you use frames (which is a common way that Frontpage allowed you to create webpages) then this can also make it difficult for search engines to decide what your individual pages are all about, and more difficult for the search engine spiders to actually follow the links within your website. Try creating your pages without the use of frames where possible, it will be a whole lot easier for the many search engine spiders out there to index your website.

Generally, JavaScript is not search engine friendly especially when it is used on a site's navigation scheme. Moreover, JavaScript is prone to abuse and the biggest abusers are adult and gambling sites. There are instances when multiple windows would open and if you try to leave a window, another window would open. Other forms of abuses are automatic redirects and the hiding of spam techniques. However, there are simple JavaScript codes that can be crawled by search engine spiders.

If you're intent on using JavaScript within your website, and are not experienced with programming in JavaScript, then try something like the jQuery website - these are pre-built, and tested across the major browsers - and free. You can download themes, or even custom design one yourself to suit the colour scheme you have on your existing site. Overall much less of a learning curve.