I already regret writing this much, boring i know
First, Let me get your compatibility concerns out of the way.
Don't worry about it.
Very long answer:
When you buy a pereferal, you get the driver on a CD or the driver is already included with windows, a driver is software developed by someone who knows how this hardware works and knows how to speak its language, and translates everything the operating system says to the "Gadget/Pereferal's language, and the other way round.
For example, to scan an image, some driver+software has to be there to send the commands to Scan, and it has to be there to receive the answer, once the input (To the computer) is there, it is a file, usually something windows/Linux can deal with like a JPEG or a Bitmap image.
When you want to print something, Windows or whatever OS you are using spools that thing, then the driver picks it up and translates it to the printer's language then it is no longer any of window's business, So the OS is the boss, the driver is the secretary.
Your Ipod on the other hand is an external mass storage device that stores MP3 files along with XML data etc... the software (Itunes) has to know how to store the MP3 and how to compose the XML file that tells your ipod everything about the file, On your computer it's just another MP3.
Every gadget you buy comes with One or more device IDs (You can see those if you go to device manager, then you chose to see the properties of the Hardware, then Details Tab, then hardware IDs), Each and every one of them needs a driver, Sometimes and in very rare cases, one driver manages more than one (2+ instances of the same software). so your HP things do not really talk to each other much.
Your hardware, having the drivers that came with them do the talking, they no longer need (And do not) care what PC is there, as long as it is there running those drivers, USB works the same no matter the brand, Same goes for Serial port, Parallel port, PS2, Ethernet, etc...
Please excuse me for elaborating this much, Let me conclude this one with the bottom line.
I personally prefer Intel main boards, There are other chip-set manufacturers who are Just as good, (NOTE: HP or Dell do manufacture chips, but not the main ones for the PC) HP assembles 3rd party chips in a very organized way, They do make better computers than the one you assemble from a cheap casing where ventilation and air circulation are not so well designed, and may be inferior in terms of vibration, Cooling, even looks, But they do the Job fine, and i use them all the time with no problems.
Now since HP or Dell or any other leading PC manufacturer does not manufacture the main chips, the can not control how the chips function, and those chips are available in many other brands (They are not tailored for HP or Dell or gateway).
Conclusion: See short answer
Now, to is refurbished computer worth the money.
As a software developer who's job is somewhat close to the hardware (Programmers don't all do the same thing), i would say you need to inspect the computer you buy, The hard drive's S.M.A.R.T. attributes, the monitor's brightness/color, Also check what problems others are having with this particular model on the internet, BIOS incompatibility with some of your cards, The Fans etc...
Case scenario: When the previous owner decided to clean the CPU heatsink, he/she took it off, used a blower or vacuum cleaner, Put it back exactly how it was, then started the computer, all seems fine, but if you press the computer to the limits, it will probably overheat since the thermal grease between the Heatsink and the CPU is no longer efficient.
Conclusion: If a used HP computer costs as much as a new (DIY) computer, go DIY, There are plenty of good mainboard manufacturers, and you get choices for hard disk, DVD (Lightscibe or not), What VGA card you need and what is an overkill, etc..
If you don't know how to do it yourself, get the neighbors son to do it for 10 bucks.