Some experience-based recommendations:
I'm just curious, which method is most durable?
Steel cable like this is excellent for durability. But it is much harder to manipulate into the non-looped over-then-through formation. In general this formation is difficult to anchor and particularly unreliable if the pole has a round cross section - due to slippage. The over-and-through looped formation is very good (even with round poles) as long as the main tension on the line is in the correct direction. Both of these are particularly useful as ends of a single tzuras hapesach. But if a) a pole is "double counting" (i.e. constituting a corner or other meeting of two neighboring tzuros hapesach), b) the pole is made of wood, and c) the line is sufficiently malleable then the around-the-nail formation is easiest to construct and most durable.
Which is usually used?
Anecdotal observations tell me the nail-in-top way is most common when using wooden poles. Of course, many industrial eruvin are constructed out of synthetic materials, and in many cases do not attach the line to the upright at all, but have it pass over the top (sometimes with no contact).
could I drive the nail/thumbtack all the way into the wood?
[ Ask your local orthodox rabbi, but ] Yup.
By the way, what material makes a good eruv string? Twine? Fishing line? Nylon?
Certain situations call for each of these. Fishing line is excellent because of its potential to be pulled taut. (Too much sagging would invalidate the line.) If your system needs to be lightweight and/or unobtrusive it is ideal. However sometimes visibility is a plus, especially if the line needs to be checked and is far away from the vantage of the checker. In this case, striped lightweight nylon cable is often employed - once again for its tensile strength. Anchoring and attachment to poles or other structures is an important consideration in choosing materials as well. Very rarely one comes across a case where it is advantageous for the line to be taken down easily, in which case carefully administered twine/string could be your best bet.