For a custom built rackmount case 2U is what I would go with, it will provide you the flexibility of using most components while still keeping your cost down per U if you are looking to colocate. Only things you will need to watch out for is cooling components, you most likely will not be able to attach a standard CPU heatsink/fan. A 4U case of course allows for much more room and the flexibility to use whatever hardware/cooling you want but if your going to colocate something that large the cost per U is pretty high.
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