I used to use 2500ton PDCs, but I find it annoying how they tie up commanders and clutter my list. So lately i've been building 10000 ton PDCs. Also, I found that transporting PDC components is not nearly as big of a deal as i thought it would be.
I also prefer to use 0.25xsize 100x reload missile launchers. These have a few advantages. Civilians do not look at reload times for PPV, so the more tubes you have the more impressive the base is. Second, you can generate much larger salvos. Third, missile silos just seem so in character... xD
Fourth, a salvo-based PDC is a lot harder to turn against you if it gets captured, though I've never had an NPR land ground troops on me.
The problem of course is that minaturized launchers require research.
Another consideration is the use of a powerful active sensor. Tonnage isn't really a problem for PDCs, and it is good to have early warning of enemies approaching your planets. These large active sensors also work better in either a larger PDC, or a dedicated sensor PDC. For similar reasons, I use a anti-ship design with a 100-res sensor and an anti-missile design with a 1-res sensor. Once you develop these sensors you can also use them for scouts, jumpships or flagships.
Zulu class Planetary Missile Base 20,950 tons 697 Crew 1439 BP TCS 419 TH 0 EM 0
Armour 5-67 Sensors 1/256 Damage Control Rating 0 PPV 128
Troop Capacity: 5 Battalions Magazine 512
Cellular Launch System (128) Missile Size 4 Rate of Fire 4000
Goliath-48 (4) Range 115.2m km Resolution 100
Shrike-25 (128) Speed: 30,000 km/s End: 31.2m Range: 56.2m km WH: 4 Size: 4 TH: 100 / 60 / 30
SPY-256 (1) GPS 25600 Range 204.8m km Resolution 100
If you take out the PDC barracks this design goes down to 8300 tons and 1300 BP. The downside of this design is that bad luck will result in a premature knockout - it only has basic PDC armor. Small PDCs have redundancy advantages. That is another reason it is designed to salvo all of its missiles at once.