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I used to build custom PCs for the 3D gfx industry (competing against SGI) a gaming graphic card is a must as an increasing number of programs make use of GPUs but rarely if ever onboard graphics chips. nvidia or radeon though? have competing GPU options and nvidia seems to be more suited but personally I've never found their drivers to be as stable as radeons. Still in practice with my astrophotography it means nothing, i dont care if the software I use uses my gfx cards or not its the processing and results that important, my computer is permanently on so no big deal to leave it processing overnight or while at work.
I've used high spec laptops with as good or better specs than my desktop at the time and none could compete in practice with the actual work of the desktop, regardless what benchmarks say.
I've always used multiple hard drives to improve performance too as described already. One for operating sytem and programs and a second for data at least. Isolating the OS onto a dedicated physical drive is important as windows is always doing stuff needing drive access plus all the malware you are likely to have too. Likewise a dedicated drive for the pagefile and temp scratch space used by Windows and programs keeps all that traffic away from anything important. Both these drives can be smallish and speed is important here. a drive for temp page files can be regularly full formatted to keep it clean and ensure its not developing corrupt blocks. Programs and data could be partitions on a large drive. This way if windows crashes or get virus infected, and i can be 99% certain it will, your best course of action if to reformat and reinstall windows. Then data is kept intact, some programs might still run without reistallation but at least they and maybe their configs are safe so getting back up and running is quicker.
Be aware astrophotography uses a LOT of hard drive space and even more for the intermediate step files (not unusual to have over 500GB of files to delete after processing ONE image) and that is a huge amount of I/O operations on the drive. So be prepared to lose everything on the drive you process with, dont store anything you dont want to lose on the same drive.
For storage get yourself a NAS unit with slots for drives so you can expand its capacity later, start with just one large drive in it.
CPU you want high GHz (raw grunt basically), quad or oct core , lots of RAM plan on filling the motherboard and use quality brand ram if you skimp to save money with "equivalent" components you are wasting money. A good monitor too and colour calibration device like a Spyder is a must. I can recommend the Dell Ultrasharp range of monitors, I use a 24" at home and our office uses the 27" ones. Fantastic colour accuracy out of the box and edge to edge/corner to corner brightness and colour consistency from angle viewing angle.
BTW with all the above recommendations you also end up with a kickass gaming machine. It will be costly too but rock solid and dependable. Overclocking? Don't bother, if you're that impatient and want to risk a fire you'll do it anyway and nobody in astronomy cares how fast you can push your CPU. My machine is 5yrs old since its last upgrade and still rock solid and gaming it doesnt break a sweat. I do run out of ram and push all 8 cores to the max regularly, data processing has killed a few 2TB drives but I havent lost anything and don't feel any need to consider an upgrade in the foreseeable future. It could be improved with SSD drives but I don't feel they are proven yet for long term reliability.
If you want a purpose built machine then stick to using it for that purpose and nothing else. The more you install the slower the operating system becomes and uninstalling never removes everything so you wont get back lost performance.
Cooling, can be good if you live somewhere with winter and summer extremes but water cooling not really needed. Just remember hot air rises and dont place drives or cards up against case walls or other hot components, keep as much airflow space around things as possible, tie back cables so they dont block airflow.
Power supply, 1000W should be fine and you can get them with cable sockets so you just plug in the actual power cables you need (they come with a kit of them) instead of having a huge ugly bunch of cabling in your computer blocking airflow.
Laptops can be useful, particularly for capture (good usb3 and SSD drive helps here) and maybe for sorting stuff in front of tv but not really for processing, they generate a lot of heat and that also shortens their lives when running them flat out. a good desktop is the correct tool for the job.
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