Hi Lindsay,
You might be interested in this: http://www.merseysidebiobank.org.uk/ws/livesites.php, my first attempt at integrating NBN services into our website, if it looks like the kind of thing you might like to do (or an aspect of it) i am happy to provide info/code.
I should stress it is my first attempt! and on starting this i had no experience of php or javascript and little of general web design, so it is very much a work under regular improvement, though may be useful to you as a starting point.
A few points to note, the sites list on the left is populated from an NBN query so for this aspect to work you would need your sites to be available on the Gateway. However, it would also be possible to set it up to use polygons you define (from your own GIS for example), and i am currently working on a new project that uses user defined polygons drawn on an interactive google map (if you like i can show you the current working bones, but it is currently very un-friendly!)
Selecting a site will produce a taxon group list then selecting a group will produce a species list, these lists are produced with queries using the site boundary so creating site specific species lists (what you're looking for?).
A species selection then shows a 1k distribution in the local area and provides links to the species on other websites (ARKive/Wikipedia).
If it times out be persistent with it, our server is a bit slow and i think i have tried to do too much!
Natural History & Biodiversity Data Enthusiast