If I remember correctly (it's a been a while), Empty Houses serves as a (very mild, and somewhat wacky*) pseudo-prequel to the Terrortory series.
There's also a two-parter of sorts in Facing Facts and We're Off to See the Wizard, which aren't connected to the plot of Empty Houses/Terrortory (think that's right...)
The rest of the missions should be playable in any order.
* Empty Houses was a cross-genre experiment, introducing telefantasy elements into Living Spycraft. It worked for some, not for others.