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All depends on what you're doing. Cram watercooling into a SFF lan rig? DC will save space. Ghetto loop sits under your desk? AC pump (with no relay) is a lot cheaper.
If you pay for your own electricity, remember that an efficient DC pump will use $30+ a year less power than an AC pump. Factoring in the cost of that relay, how long before the DC pump pays for itself?
That's up to you to decide. I prefer 12v pumps over AC pumps mostly because of size differences. The only popular AC units that come close to such pumps as the Swiftech MCP600/MCP650 would be the Hydor line of pumps. Even then, they don't seem to perform as well as their DC counterparts. Thrown in a prebuilt relay and you have approximately the same price as a DC pump. Since you're creating your own relay, an AC setup would probably be cheaper. But then, you have to consider the time spent making the relay, where to mount the relay, and how you're going to get power to the pump. In my opnion, 12v pumps are wirth the extra cost.
I switched to a 12v pump (MCP600) a while ago, and I really like it. It is very convenient to not have to worry about a relay or extra wires. Leak testing outside a machine gets more complicated, but since I have a large supply of old AT powersupplies around, I was set in that regard.