The price of CAT6 has dropped to the point where it is probably a better choice than 5e in my opinion. Be wary of CAT6A or "augmented" which is a step up from regular CAT6 however. The RJ45 connectors that are CAT6A rated are significantly more expensive and trying to terminate 6A with a regular RJ45 connector is not recommended (trust me on this one!). Multiple runs will allow for multiple options at install (for example: segregating your data network, or using 1 cable for data and 1 for voice, etc.). In hindsight, I would recommend 3-4 CAT6 and 2 RG6 to each drop. This is coming from someone that just ran 10k feet in a 3700 sq ft new construction project as an owner builder.