Yeah I guess you got it.
CPU : i5, or i7 if you're gonna build massive software often. In any case chose the Haswell K series (model number 4xxxK). These are the latest and K means you can OC it so you can freely upgrade. Also get a good cooler, Intel's sucks ass.
RAM : 8 or 16GB. 6 is definitely not enough and should only be used with triple channel setups anyway. PC3-14900 is the speed you should take as it's a good speed:price ratio.
SSD and HDD : You pick. A typical setup is SSD for the OS and HDD for mass data storage, so 64 or 128GB and 1 or 2TB.
GPU : If you don't plan on gaming (recent games) at all, then none. The new IGPs in Intel CPUs are very good. Else AMDs are cheaper than Nvidia so if you don't have a personnal preference go for AMD. Pick the best one that fits your budget.
Mobo : The key to chosing a good mobo is the chipset. You probably want the Intel z87 since it's the best one for custom built PCs. Then any brand will do. Your budget and the specificities each mobo has will help you picking the right one.
PSU :
http://www.extreme.outervision.com/psucalculatorlite.jsp will help you pick the right wattage. Give yourself some upgrading margin in the specs you input. Looking for 80plus certified PSUs is also a good idea but not necessary. Also please don't pick a random no-name one.
Hope it boils down what you wanted to know. I tried to be as objective as possible here.
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