From my experience with analog stereos, cables do make a difference at all stages. If you want to get some interesting reading, check out MIT Cables www.mitcables.com and read their variety of white papers.
Obviously, cost is an issue, but MIT does have cables at different price points.
I have been a long time fan of MIT for years and have positive experiences with their products. What they are doing is essentially putting in passive networks to make as neutral of a cable as possible. They also have a USB cable that goes from USB A to USB B cable for the connection between the computer and an outboard USB DAC. I just ordered it so I should be recieving the product in a day or two and I have to allow it to have a couple of days of burn in.
But, yes, cables do make a difference, but sometimes for the worse. When transmitting analog signals, not all cables are actually transferring the entire frequency spectrum at equal levels, so some frequencies that are being hindered willl make the cable sound differently. This goes for interconnects and speaker cables.
Depending on which cable you get and the rest of the audio chain will determine if and how much difference you will hear, but ultimately we want the cable to not alter the signal in terms of transmitting frequencies differently that can make the audio sound harsh, dull, etc.
What I suggest is go to MIT's web site and read the white papers. It might take a few readings to allow the information to sink in and they also have a nice video explaining this that is also helpful, and then it's a matter of picking the right cables for your needs.