I use vanilla to run multiple sites.
I use one control panel to access all sites and share the thumbnail database with each site. If thumbs are all of the same size it means I dont have to thumbnail thousands of galleries for each site but instead export what ive thumbed for one site to all sites.
It has a bit of a learning curve but this is only because of the massive amount of options it comes with. I was a complete script noob when I started with it but it didnt take me long to get the hang of it.
The personal support is top notch through their forums, help desk and IM, and the software is being constantly added to and refined based on user feedback.
As for other scripts, mine plays very well with Arrow Trader traffic trade scripts. The vanilla forums have some help threads on how to install the code, its pretty straight forward. And of course it works with all major trade scripts, to my understanding.
Well, sounds like an ad but Im just a happy webmaster
http://www.vanillatgp.com