Another approach would be to embed the flash movies inline and hide them. This will allow you to use unlimited number of different sizes as set by the style attribute of the wrapping div... But I'm not sure how auto-playing SWFs will behave in a hidden div so you'll have to test.
An example of a hidden embedded flash movie, to be opened with fancybox in inline mode:
<a href="#Unique-ID-1" class="fancybox">open my movie with Unique-ID-1</a>
<div class="fancybox-hidden"><div id="Unique-ID-1" style="width:240px;height:600px;">
<object ... [snip] and the rest of your regular flash embed code here [/snip] ... /object>
Use a different ID for each new hidden flash file and set the style attribute to get your different sizes. And if this is the only way you are going to use fancybox, you can disable all features except the default 'Images & Inline content' and remove all file extensions from the Auto-detect field to improve on page load speed...