Selecting the preferred pickup for our guitars is a trial-&-error process really; there isn't a definite guide to what really works. The manufacturer's tone samples & EQ charts are fundamental guidelines to our pickings; these serve to sway us in the right direction but the ultimate satisfaction comes much later when we hear them in action. Thusfar, the pickups I've acquired are good matches for my guitars, I am often asked how do I go about choosing what I want & ending up being happy?
Pickup = microphone
In its fundamental form, the guitar's pickup is virtually a specialized microphone. Pickups are electronic devices which simply 'pick up' the string vibrations & transfer them to the amp. Different pickups according to the component make-up (magnets, wires, pole-pieces, etc.) across brand names would yield different tones. It is therefore the immediate voicing factor which would shape your guitar's sound through the amplifier. It is then necessary to understand the various pickup character & matching it to your guitar for best results rather than choosing the flavour of the moment & keeping your fingers crossed.
Remember your guitar
The critical factor which we overlook when we go pickup shopping is our guitar consideration. The objective of having a certain pickup make in our instrument is to complement its inherent resonance. Many of us failed in this aspect because we choose a certain pickup to influence our guitar to sound a certain way, more often than not, the way we want it to sound like but if we do not possess the right guitar with the desired tone in the first place, it's not going to work regardless of the frequency of our pickup replacement.
Hence the first crucial step in pickup buying is to listen to your guitar, unplugged. Listen to the unamplified tone & scrutinize accordingly- is it deep sounding? Too bright perhaps? Bland/ neutral sounding? Lacking midrange? It is worth making the extra effort to compare the inherent tones of Guitar A &Guitar B just to hear that difference- it's this comparative difference that helps us better understand our guitar's tonality.
Two-prong consideration
You can then consider the various pickup offerings out there, keeping your guitar's acoustic properties in mind- this is crucial. Refer to any manufacturer's homepage & look at the tone chart for the different pickup makes & their respective EQ specifications. The recommended approach here is to pick the pickup (no pun intended) which complements your guitar's resonance. Say if you guitar is trebly, the pickup with strong upper frequencies would do it good more so than others. Sounds like an overdose, yes? But that's what I've learned along the way. I had a Seymour Duncan Invader in my Ibanez S540 sporting a satin finish, thinking the pickup's strong lower frequencies would counter the guitar's inherent brightness but this matching manifested some bland results, resulting in a loss of character & single note definition under high levels of distortion. The current replacement in the afore-mentioned guitar is a Duncan Parallel Axis Trembucker which complemented the instrument's marked midrange. Any frequency excess should be trimmed via EQ (amp/ pedal) settings.
The other approach would be purely the selection of pickups based on the (manufacturer) specified EQ. This is rather dangerous as the guitar's inherent resonance would displace the pickup's voicing, resulting in limbo tone- one which bears no inclinations to both the guitar & pickup characteristics.
Wish that...
Choosing pickups is no easy venture. As a sure selection doesn't exist, we exercise referential picking in the hope that what works for a particular guitar would work for our guitar of similar properties. We wish there would be an easier way to go about doing this in time to come. Some dealers/ manufacturers exercise a return policy but this practice isn't universal. 
