I once realized something like that, however without using fancybox. But I think, the idea could be helpful.
On an overview page I listed the galleries, each represented by an randomly chosen thumb:
[!Ditto? &parents=`[*id*]` &sortBy=`menuindex` &sortDir=`ASC` &tpl=`EG_TeaserTpl` &display=`999` !]
The chunk EG_TeaserTpl:
[[EvoGallery? &docId=`[+id+]` &display=`images` &sortBy=`RAND()` &limit=`1` &itemTpl=`tpl_EG_overv_item`]]
The chunk tpl_EG_overv_item:
<div class="floatbox">
<div class="thumbscontainer">
<ul class="thumbs">
<li>
<a href="[~72~]?picDataString=[+content_id+]~[+id+]~[+filename+]~[+title+]~[+description+]"><img src="[+thumbs_dir+][+filename+]" alt="[+title+]" title="[+title+] ~ [+description+]" /></a>
</li>
</ul>
</div>
<h3><a href="[~[+content_id+]~]">[[GetField? &docid=`[+content_id+]` &field=`pagetitle`]]</a></h3>
<p>[+description+]</p>
The page with all the thumbs had this EvoGallery call:
[!EvoGallery? &docId=`[*id*]` &display=`images` &sortBy=`filename` &tpl=`tpl_EG_all_thumbs` &itemTpl=`tpl_EG_thumb_item` !]
The chunk tpl_EG_all_thumbs:
<div class="floatbox">
<div class="thumbscontainer">
<ul class="thumbs">
[+items+]
</ul>
</div>
</div>
The chunk tpl_EG_thumb_item:
<li>
<a href="[~72~]?picDataString=[+content_id+]~[+id+]~[+filename+]~[+title+]~[+description+]"><img src="[+thumbs_dir+][+filename+]" alt="[+title+]" title="[+title+] ~ [+description+]" /></a>
</li>
The page with ID 72 was the page to display a single picture. I used jquery-cycle here, but that should be easy to modify for fancybox. The template of this page contained this EvoGallery call:
[!EvoGallery? &docId=`[[getPicFolder]]` &display=`images` &type=`jquery-cycle` &tpl=`tpl_EG_img_cycle` &itemTpl=`tpl_EG_img_item` &sortBy=`filename` !]
It's a while ago I did this, and I'm sorry not to be able to go deeper into details. Hopefully it might give you an idea, anyway.
