Since you asked, I'll throw in a couple of thoughts...
I'd consider springing for 8GB of RAM - it should only be $5 or $10 more if you don't go for premium memory. I have 4GB in my box and it's more than enough to run any Linux distro, but I find myself a bit RAM-limited if I want to run Linux or Windows in a VM.
Also, are you sure you want to go mini-ITX? Compact cases are all the rage now, but they do limit your future upgrade opportunities and I find them much harder to work in. You might find the additional space inside a mini tower case easier for a first build.
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