If you've got 3 axes, and limit and home switches for each of them, it'll add up to 9 switches in total - so you would need an extra parallel port.

But since you shouldn't ever really hit your limits, you should be able to get away with all the limit switches to one input, and you could put the home to three other inputs.

I can't comment on the Mach3 side of it though, but you can wire them in either series or parallel - series is the traditional way of doing it, as there's less wiring to go wrong (and it also means there's a fail-safe, so if your wiring breaks, it'll end up thinking the limit's been hit).

To me, microswitches are the obvious choice, but I'm toying with the idea of a magnetic switch of some sort, so there's no physical contact (I'm vaguely looking for an optical solution for home switches though). Get ones with rollers on, and make sure there's a gradual slope for them to switch (otherwise if there's a bit of momentum, you could bend the lever).

The advantage with microswitches is that they generally have normally-open and normally-closed connections, which means you can choose between series and parallel connections (normally-closed connections are used for series, normally-open for parallel).