1) Usually use Skype.

2) Yes -- chat-wise Skype is absolutely fine though

3) I would love the ability to have longer term centralized storage of the chats with a decent search engine and the ability to have scripts post stuff as well.

As far as I can tell the best alternative is setting up an IRC service: it'll run within your corporate environment if you must, easy to integrate deployment scripts into (&c) and there is a lot of archiving/search apps already.