Well, they are not working together so to speak, but you can see more and more compatibility between mods appear with the versions going out.
I mean, RP relay and engine are a good example of that, from the author that only works by herself and does not go out off her way to make that usually.
For some mods, it comes from plugins, like how Forestry (was a BC plugin early on) made it possible to use EU to produce MJ, and use fuels to produce EU.
Forge and its side-specific approach of the inventories also make it possible to use BC pipes on any forge mod that remembers to code the sides (not really hard or long thing to do).
As OmegaPython said, the ForgeCraft server (previously called PahiCraft) also serves as a test server for a number of authors, and they can test various mods combinations and see what works, what doesn't, and fix what can be before the public releases.
Well, I suppose that having played with mods for more than a year and half now, my opinion is based on the fact that they play way better together as a pack of mods now, compared to when you even had troubles installing them together.
Perhaps you could give us a more precise description of what "play a little nicer with each other" means?
