Try looking into clusters. Now that is worth building I don't own a custom box, but most people I know got them. They love them and buy accessories for their towers. Big cooling fans, even neon lights, do you have stuff like that too?
Custom computers can be cheaper and more affective but in the end anything purchase from a company for example dell is professional setup and checked and which point if something is not working you can return it as for custom you build yourself and isn't really good if you don't know what your doing.
Don't use a system unless I built it. too much of a headache buying them manufactured. That way I know exactly what to upgrade and with what. Right now if I want to upgrade I go to Compusa get a new processor and drop it in in two minutes all because I chose the motherboard with an easy upgrade path. Something goes wrong I know exactly what to replace.