That's an incredible value and it seems like a fine system. I don't see reference to what it has for video card but according to what you said earlier, you're just running the one monitor, right? I'd definitely spring for the new and not the refurb. Just a personal thing.
Windows 7 itself doesn't use up that much disk space. At least in today's environment it is not a whole lot of disk space. I have a 40GB SSD for the OS drive. It has 2 copies of the Windows folder (one time re-installation of Windows). Windows 7 takes about 12GB or so. If you have some of the big applications - such as Adobe... the whole CSx suite, that alone may take up 7 to 8 GB. Disk space is cheap now. I echo that. It is so easy to get a 1TB disk. Or at least 500GB. Unless you are on SSD that you may be bounded to smaller storage. At any rate, having only one big disk... it is a good practice to partition your physical drive into different partitions, then mount them as different logical disks. This is so if you have a runaway program filling up the drive, you can confine it to only the data partition and not have it causing Windows have difficulties running. e.g. if you have a 500GB drive, you can partition it as 50GB or 100GB for OS and apps, then the remaining 400GB for data storage.