Placement of Through Hole with a High Tolerance Dimension
If the location is really, really critical you can have a jig fabricated that will hold the part in place during soldering (relative to some other features on the board). That's not uncommon for things like LEDs that need to be precisely located or they look bad or won't fit into molded holes etc. You'd then probably want the hole a little sloppy, but not so sloppy that joint strength is unduly compromised. 

Usually the component manufacturer will have a recommended hole size, and in my experience it's usually quite sloppy so that automated insertion equipment will never fail. 

If your pin is round you need a bit more slop than if the pin is square or rectangular. For example for a 0.25mm square pin, the recommendation might be 1mm+0.1/-0.05mm for the hole (ideal diagonal distance is \$\sqrt{2}\cdot 0.64\text{mm} = 0.905\$mm but in practice 0.9mm nominal hole actually works well for manual assembly because the corners are a bit rounded and if there is a bit of interference they can move the plating a bit. If you actually measure a typical 25 mil square pin with calipers you'll probably get about 0.85mm. 

Officially, the difference between maximum pin diameter or diagonal and minimum hole size (taking into account both tolerances) should be 0.15, 0.20mm or 0.25mm depending on IPC level. If I do that calculation for a Molex 25 mil pin, it's maximum 0.68mm so the diagonal is 0.962mm so we add 0.15 to 0.25mm so 1.11mm to 1.21mm minimum. Now we need to take into account hole size tolerance- say +0.13/-0.08mm. So we need to make the nominal hole size 1.19mm to 1.29mm. That is really sloppy. Molex recommends 1.02+/-0.05mm for this particular part 470531000.  

So if you use the recommended connector manufacturer hole diameters you'll probably never have a problem inserting the part (but it may be pretty sloppy) with any modern PCB supplier, even an inexpensive one. 

For a 0.5mm round pin, JST, for example, recommend 0.7mm +/-0.03, and non-cumulative tolerance on the hole locations of +/-50\$\mu\$m (that means that the centers are within 0.05mm of the nominal position whether there are 2 holes or 20 in a row, not 19 * 0.05 which would allow the end pins to be almost 0.5mm off). If your PCB supplier does not maintain that tolerance you should use larger holes to compensate. If you like living dangerously, 0.1mm nominal delta between nominal pin diameter and nominal hole size will usually work and has a much nicer feel when doing hand assembly but there's always the chance it won't. (of course, have a plated-through hole too small is a disaster and likely requires re-spinning the board, you can't just drill them bigger).