Media Center Build ?s, pci, gpu, etc

Building / buying an older pc to turn into a media center. Running plex home theatre, maybe plex server, hyperspin emulator setup, maybe a few other games etc, nothing crazy. Looking at craigslist, ebay, etc for a cheap i3, i5 set up, and then upgrading with ram, gpu, and a loooot of big hard drives. Built a few systems, but not in years.

My questions in regards to gpu are, if i buy a pc with integrated graphics chip, i cannot upgrade the card later, so need one with any dedicated graphics, then swap out eventually. Are there differences in pci types? in other words can any pci card be swapped for a newer pci card, or do i need to look for something specific with the original card/mobo?

In the same respect, I plan on putting extra hard drives, have 10+TB media, some external hds, etc, but do I need to look at anything specific on the mobo/pc to make sure I can add bigger/more drives?

finally power supply issues, is this something I can upgrade after the fact on a system like this with a stock case etc?

thanks all!

few examples ive seen...
http://www.ebay.com/itm/HP-8100-Eli...554383?hash=item3f57e4d5cf:g:fIcAAOSwv-NWVzk1
http://www.ebay.com/itm/HP-Z200-SFF...121818?hash=item25b1f08c9a:g:cEUAAOSwFGNWS5iQ

Not true. A PC with integrated graphics almost always can be upgraded. The usual setup is this: Have PC using integrated graphics. Inserting a new graphics card in the motherboard disables the built in graphics. You need PCIe x16 slots to install a new graphics card. It will not matter if it is version 1, 2 or 3 for your purposes as an HTPC.

Some AMD motherboards allow you to xfire the built in graphics with certain addin cards.

Motherboards will come with multiple SATA ports for HDD/optical drives. Generally speaking, I think that the average motherboard comes with six SATA ports. So, 1 blue ray for purchased video and 5 hard drives. The size of the drives depends on the OS you are using. 32 bit OS maxes out somewhere around 2 TB I think. Otherwise, you can generally get away with any size out there. You will want SATA II or SATA III. The new the better due to increased speed.

Power supplies are fun. I would get one that is 80+ Silver or better to reduce heat and thus noise. For a simple HTPC setup, you could easily get by with a 400 watt PSU.

EXCEPT!

The two examples that you selected are less upgradeable due to the size of the case. If you select a system with a small case, you will be extremely limited on all upgrades. A full size video card will not fit. An off the shelf power supply will not fit and may be proprietary. You may only be able to install one hard drive. The size of your case would be your biggest limiter.