Difference between Sildenafil and Sildenafil citrate
In many pharmaceuticals (and many recreational drugs) the choice of form is determined by the convenience of the manufacturing and delivery

Many drugs (not just sildenafil) are manufactured as salts or simple derivatives of the active molecule. For example, the anti-inflammatory steroid fluticasone is usually delivered as the propionate or furoate esters and the recreational drug cocaine is usually delivered as the hydrochloride salt. In all this cases the active ingredient is exactly the same in the body.

But there are two factors that matter as well as the active ingredient. 

One is how easy it is to obtain a convenient form that is pure and easy to make. Amines, for example, are much less prone to produce nice crystals than their salts (sildenafil and cocaine are amines). Since the industry needs to have a good route to a verifiably pure compound and since crystallisation is a good way to obtain pure compounds, they often experiment with different salts to find one that gives a satisfactory end result. This is convenient for the manufacturer and makes no difference to the active ingredient which is determined by the pH of the biological environment.

The second reason is the ease of delivery of the drug. The physical form and chemistry of the substance or salt do matter for the bioavailability. If the drug is taken as a pill, it has to be well absorbed in the digestive system (which means it should, usually, dissolve quickly in the stomach). Salts are more likely to be rapidly soluble than simple amines (though this depends on the form as much as the fact they are a salt though the form is more controllable if you have nice crystals to start with in manufacturing).

The illegal drug cocaine is an interesting case. It is easy to maufacture it as a salt and it is commonly available as the hydrochloride. The hydrochloride dissolves in nasal linings giving a high. But some prefer a faster, more intense (and also, unfortunately, more addictive) high obtained by using the vaporised freebased amine. This is easy to make by reacting the hydrochloride with household baking powder. But it can't be sniffed in that form (as a powder), it has to be heated and vaporised for effective absorption. The vapour is absorbed more rapidly directly into mucous membranes, making a faster hit. But this isn't as convenient as sniffing a finely ground powder and would not be a convenient way to distribute legal pharmaceuticals (imagine the police attention if you had to heat a spoon full of fluticasone to relieve your blocked nose).

So, in short, convenience of manufacture and delivery frequently lead to the ideal form of a drug being a salt and not the pure active ingredient.