hmm this ones easy... i tried and tried until i found my perfect combination 
try to get atleast 1 trade port per planet (not massing them on 1)
so every roid should have atleast 1 trade port too!!!!
every 3 or 4 planets.. u give a culture structure.. this supplies a steady and fast culture to your inner empire
add cultureal buildings at or close to the border that is under cultural attack, also try to station capital ships there (vasari get a bonus here) (for those of you who dont know, capital ships have influence and lower enemy culture)
all large planets (deserts , terrans) should be given atleast 1 culture center, 1 trade port, if its a major hub, adding a dock wouldnt hurt either (should only be done if you think it'll be used or if its on / near a border)
adding a 2e trade port to deserts is a good econimical choice, but will hurt your research center capacity.... choose carefully... (big maps are not a problem)
in case you play as vasari or TEC you have Refinery's, this parts a lil more advanced tough... and needs a good overvieuw of your empire, bordering planets and a good sense of wether it'll help or actually hurt progress
search planets wich have alot of bordering colonized worlds (or neutral extractors) place a refinery at that world, refinery ships wil harvest extractors up to 1 phase jump away, every PLANETBASED extractor has capacity for 3 bordering refineries (neutral extractors have 4) check and calculate closely wich planets will have the refinery bonus, if you do it right you can have 80% of your empire's extractors coverd with atleast 2 refinery filled slots
total recource income should get around a 50% bonus (this is a guess, i never actually took the time to calculate this.. any reply on the % is welcome 
remeber that refinerys need carefull planning, it's highly possible that you'll have 1 refinery per planet, but in some planet "webs" you'll be able to get a small number of refinerys that still cover 80%... planning and learning is key
all remaining planet slots should be filled with research center .. example: you still need 2 economic centers and 4 combat centers, place them preferably somewhere behind or deep inside your empire,
if you've got the maximum centers you can start placing more refineries (trying to get quotes of 3 or 4 (having a planet with 4 quotes aint a problem if you'll fill another up to 3
after you feel like the refineries r about right, start placing culture centers, trade ports and on the borders, docks
thats about it
remeber that everything stated here is for long games.. if u prefer to rush dont bother sticking so much time in economy this is however my playstyle on large maps... since rushing there cant really be called a rush