Sounds good, but one thing is that I do think we need a file server / file share or peer-to-peer based sharing mechanism as well. I want to run a several instances on one computer as well as other instances on other computers on my home network and have them all share without having to run a local database server or web server with PHP scripts. Allowing for a bunch of instances provides environmental locality, barriers to migration, etc. and I hope to see different species dominate the different connected ecosystems.
That said, with a real server, we could provide a means for lots of cool collaborative features such as collecting and presenting global population information accross the connected sims, global dead and born counters for each species, etc. (Although there are less robust ways to do this using FTP or similar.) Microsoft's Terrarium did this and the competitive aspects really spurred organism authoring. That is, seeing at a glance on a web page how many nodes are currently connected and which bots have the highest population numbers in the connected ecosystem motivates one to attempt to author a better bot and become top dog (errr, I mean top bot).