I used to plant my first citizen on my home world.  If you are on a sparse map and your home world is the only one you have, that is effectively an empire wide +30% bonus.  

Nowadays, I end up building up 2-3 scientists and saving them to plant on a really good Research planet I find.  Still figuring things out, maybe.  Fun!  

One or more workers assigned to your homeworld is good for synthetic races early in the game, since you need as much social production as you can get to "build" population for colony ships. 

Yep your use of citizens has to be adapted to the type of maps you like to play on. Like me personally I never assign citizens to planets anymore, I just store them up until I unlock Leadership. I will use a few also as admins and spies. Yes that slows me down a bit at the start, but the type of maps I play on I am usually guaranteed to have 10+ planets around turn 100. That is the nice thing about Crusade, you can be flexible with how you use citizens to suit your needs.

The States/Regions  tread that was posted back in the original game could come into play here...

I think they need to have region capitols that perhaps cost a crap load to build but give several benefits..  one of which is will serve as the launch point for citizens that are assigned to closer planets.

This would give the distant worlds some viable options for getting citizens assigned...

ooh, also, it is nice taking the starting planet of a "tall race" .. I recently got 8 planetary citizens (5 of which were Engineers) on a relatively poorly defended planet (only 4 legions defending, and only took out 4/5 of mine).  Basically won the game for me.

As much as I can afford it during a long and vigorous Colony rush, I set aside 2 or 3 citizens as government scientists.  When I am convinced I have found the best Research world and gotten the hub buildings up, they move there and stay there.  90% boost on a hub world is impressive!  I make sure to park the right Mercs there and everything.  If my gang of leaders is working Research as well, it gets even better.

On a truly large map with a truly large empire, the 3% does really add up, but my feeling is that if you are at the stage where 3% counts because you have so many planets, then 6% is even better.  So, I go for Leaders a lot.  They are also good if you are conquering your way to a giant empire.  Instant bonuses to new planets is very helpful to a rampaging tyrant.

Still, pumping up an early Research planet with some planted scientists is going to pay off all game long.  And it is more important as your initial ratio of planets per player from map settings goes down.

So many choices.

I was skeptical when I first heard of the Citizens feature, but having toyed with it in the few days since I bought GC3 in the sale I think it's been done pretty well and seems to add some interesting decisions to the game. I do though have one question and one gripe though.

Question: Once I've assigned a Commader to a ship, how do I transfer them to a different ship? I encountered this situation the other night where I attempted to assign a Commander to a small combat ship, but the Commander was instead assigned to a medium support vessel instead, which was really inconvenient as I didn't have the logistics capability to have a pointless support vessel in my task force. It happened twice.

Gripe: Isn't 'citizens' a really daft name? Your empire contains billions of citizens. Surely these individuals are luminaries or specialists.