it depends what you want to do with it.
if you just want a secure base for mines and res generation go far out to some remote galaxy (7 or 8). If you wan't to use it as another base for raiding from, stay in the populated galaxies, like 1 or 2 and just locate it a couple 100 sytems away from you. If you just wan't to ship all the res back to your homeplanet then just locate it in your system, however this will mean that if someone wan't to attack you, they'll now have no problem finding your second base.
also to take into account are the average field sizes. you basically want a colony that has 200+ fields. anything less than that you will find that as you progres in the game that you will find that you simply can't build any more byuildings for lack of space, which is a bad way to be. Rember every level takes up a field. the position in the sytem also has an affect on the field size.
Quote:planetsize:pos1: average: 64, 60% between 48 and 80 fields
pos2: average: 68, 60% between 53 and 83 fields
pos3: average: 73, 60% between 54 and 82 fields
pos4: average: 173, 60% between 108 and 238 fields
pos5: average: 167, 60% between 95 and 239 fields
pos6: average: 155, 60% between 82 and 228 fields
pos7: average: 144, 60% between 116 and 173 fields
pos8: average: 150, 60% between 123 and 177 fields
pos9: average: 159, 60% between 129 and 188 fields
pos10: average: 101, 60% between 79 and 122 fields
pos11: average: 98, 60% between 81 and 116 fields
pos12: average: 105, 60% between 85 and 129 fields
pos13: average: 110, 60% between 60 and 160 fields
pos14: average: 84, 60% between 42 and 126 fields
pos15: average: 101, 60% between 54 and 149 fields
The fieldnumbers are posibilitys, different numbers are always possible

so for larger fields go for position 4 - 6. remember that the closer a planet is to the sun, the more efficient your solar sats are, but the less efficient deut mining is. so 13-15 give the most deut. 1 - 3 are good for solar sats.
basically colonising depends on your style of play. if you wan't to turtle it, you know use it for res, get it as far away out of the populated systems as possible. if you want to raid lots, stick it in the middle of galaxy one or two. it's really up to how you think you will play the game.
yeah, i'm a cranky 'oul fucker. deal with it.