Points to consider when buying your guitar pickup are it's size and pole spacing, it's impedance and it's output.
Size and Pole Spacing
The overal size of pickups is fairly standardised, so as long as you know if you want a single coil or humbucker pickup this shouldn't be a problem. The only problems I have heard of are with the special Stratocaster humbucker pickups designed to fit into the space of a single coil pickup on Stratocaster style guitars. A little enlargement of the single coil pickup hole is sometimes required because the special humbucker pickups are a little larger than the single coil hole.
Pole spacing can vary, but this is quite rare. Generally there are two types of pickup division which divide between the big two guitar manufacturers fender and Gibson. Gibson use a string spacing of 50mm, but Fender use a slightly larger string spacing of 52mm, and this is often refered to as F spacing. The difference is very small at 2mm, much smaller say than if you string bend on your guitar (a playing technique), which will push your string many millimeteres off centre. 2mm means that at either end of the pickup if the wrong type of pickup is used the string would be 1mm (half of 2mm) from the exact centre of a 5mm pickup slug, so many people ignore the difference.
This rule is for the bridge pickup – the neck spacings are a little smaller at 48 or 50, similarly different, but many people ignore this because they consider 1mm will make little difference.
Impedance is a hard to measure statistic, so most people use the less accurate resistance figure instead as a way of judging. There are shortcomings to this. The resistance is related to the thickness of the wire and it's length. You could make a pickup appear to have a higher resistance by using thinner wire, which would mean that the same or fewer coil windings would have a higher resistance and so deceive you that an inferior pickup was better quality, so beware of absolutely relying on resistance figures. The other point is that pickups have always had a set resistance for a reason, and so if you use higher output pickups that have a higher impedance this will place a greater load on your amplifiers input circuitry. The result of this is said to be a muddiness that gets worse as the pickup impedance goes up. How a pickup is wired is a trade of between ouput and impedance.
The main reasson for wanting higher output is to get longer sustain of notes, but this longer sustain will come at the expense of tone. Many people describe very high output pickups as sounding muddy, so it's important to try to find what suits your personal taste. Some rise in output is possible, but if you go too far you can wreck your guitars tone.