Holla fellow Seti cruncher!
I might not have enough time to completely explain this(class soon

isgust

, but I'll give it a go.
With impeller type pumps(the aqaurium types) used in watercooling applications, you cannot develop much pressure. So if you have a bottleneck, the pressure will not appreciably increase to allow more flow through that small radius. Basically, your smallest cross-sectional area in your entire system will dictate the flow rate for the rest of the system. This means that by going from 3/8" tubing to 1/2" ID tubing, you will effectively increase the flow in your system by about 70%(give or take based on the barbs actual ID and other small parts). You are right in thinking that water velocity plays an important part in the cooling equation. But it is actually reversed from what you said, it takes time to introduce or remove heat from water, but you want the total volume of the system circulated quickly. An easy way to do this is to use a heatercore with a large diameter flow chamber and a water block with deep channels while making sure the rest of your system is not overly restrictive.
So basically, you want to use 1/2" ID silicone tubing from Home Depot. A heatercore(or Aquastealth Aquacoil II
Aquastealth) and a good copper waterblock is also a necessity.
Try my fav WCin' links for info and products.
DangerDen
Procooling
[H
Just tell me if you've got anymore questions about this stuff. I've been researching it for a while, and hopefully I'll have my WCin' gear put in my case this weekend(it's been collecting dust long enough!!!).