Or, you can think more subtly... Capture an enemy Colony Ship... He's probably got dozens of them hanging around, so he won't miss one or two... What can I do with a Colony Ship, you ask? Well... now you have a sample of another race's population, which if you're lucky breathes a different atmosphere - and if you're even luckier he even has a different planet type so you can analyze the colony ship and steal his colony tech!
Always use the latest Version of Counter-Intel. (Unless you have a lot of points stored in a previous Version, of course, then you might as well keep it around until it expires.) Counter-Intel 2 blocks twice as much intel as CI 1, and CI 3 is 3 times as effective as CI 1!
Only use Food Contamination on smaller colonies - don't even bother with a homeworld! The population will regenerate in a turn or two and you'll have wasted 20K intel points. But if you use it on a smaller colony (<50M), you can wipe out the entire colony and force the enemy to send a transport to repopulate it before it can produce or build anything!
Conversely, use the intel that causes plagues (if there is one - I don't use intel much anyway since it always seems to get blocked
) against larger colonies, since (I think) plagues kill based on a percentage of the population, not a fixed amount (unless the population drops really low, otherwise it would take forever to finish a colony off!
)
Write down the results of stuff like Ship Blueprints and Tech Reports because this will not be updated where you might expect (known technology for an empire, known enemy designs) - though this might have been fixed for Ship Blueprints.
Never use the one that destroys resources, if you feel the urge to, use the resource stealing project instead - it's cheaper, has the same effect on the enemy, and you get resources as a bonus! (Note: some mods fix this oversight, check the mod before you try this!)
Use Crew Insurrection as a poor man's Technological Espionage - it's only 1/3 the cost, and you can get multiple technologies from a single ship! There are only two drawbacks: 1. The enemy has to have the technology you want actually deployed on a ship, not just researched. And 2. You have to manage to get the ship back to one of your spaceyards safely to get the technology!