As Vladimir said this is very difficult to interface such device. But have you actually tried to look the speed of PCIe on the internet before even considering to interface your hardware with an Arduino?
Based on information here : PCI express page on wikipedia, even first revision of PCI provides a transfer rate of 250Mb/s, which is way over the CPU clock speed of any Arduino made (even ARM-based ones). Also, such speed requires the PCI signaling to be performed with differential signaling, which is not supported by Arduino out of the box. You would need a converter to read the data. It is therefore mostly impossible to do what you want.
Longer answer with more details and explanations:
The only board that you may possess that is actually possible to interface with (apart from your HDD) might be your RAM if it is very old (such as PC33 or some similar stuff), because it was clocked and not differential, so you could be able to use it, but frankly you are better off using a brand new ram chip, it will be most easy to use and less costly.
Also, you should consider that beyond 25MHz (only 5 MHz if you want very high reliability) it is very hard to prototype on a breadboard, because of stray capacitance. As such, it would not be possible to test your stuff the way you intended it. Interfacing PCI devices it not as trivial as you might think. You cannot just hack stuffs together. At high frequencies, signal will bounce all over the place. This is why many boards contain dozens of capacitors and resistors in series/parallel with the lines: they are intended to match the impedance of the lines so that every edge is sharp. Doing this on a breadboard is not challenging: it is plain impossible and non-deterministic because parts are clipped and not soldered together.
When designing PCBs with very fast protocols such as USB 3.0, SATA, etc. it is very common to match the impedance with trial and error (it cannot be realistically computed), since it depends on dozens of factors (strip lines length, cooper thickness, proximity of other wires/strip lines, etc.). Measuring the correct value requires very expensive stuffs such as high quality multi-channel oscilloscopes that may sample in the 4-20 GHz range, which you probably don't have since they usually cost 100k$-400k$.
Bottom line: you can't do that without proper electrical interface (motherboard).
If you want to play with computer stuff while still being very low level, buy a single board computer (some cost around 100+$) and you can hook hard drives (mostly SATA, though), ethernet and stuffs like that.