Bell peppers do have different flavors if they are different varieties. However, whether they have three or four lobes on the bottom is not a determining factor in what variety they are. Certain varieties may tend more heavily toward four lobes or three, but both shapes of bell pepper may grow on the same plant. All three and four bottomed bell peppers belong to varieties that produce three or four lobes, or that produce two to five.
A page on eHow gives a detailed description of another putative difference. Three bottomed bell peppers, it claims, are male, while four bottomed bell peppers are female. Female bell peppers have more seeds than males. For this reason, eHow advises always buying “male” bell peppers at the grocery store... since females have more seeds, they weigh more, and weigh more because of something you will only throw away, making them a "waste" of money. Unless you are one of the rare few who take the time to preserve these seeds!
If there is any such thing as male and female bell peppers, the designation is culinary, not biological, and if it is a culinary designation, it does not appear to be a widespread one. Fruits (bell peppers are biologically fruits, being the seed bearing part of the plant) have no gender. They are not the plant’s sexual parts, but the vehicles for its offspring, formed only after the plant has been pollinated and fertilized. On most flowering plants, including bell peppers, the flowers that become the fruit have both male and female parts, making them androgynous. All bell peppers, then, are hermaphrodites.
No Internet sources available at the time of this writing support or refute eHow’s claim that four bottomed bell peppers have more seeds. In my own experience, having cut up many a bell pepper, larger ones usually have more seeds. Since four bottomed bell peppers tend to be slightly bigger than three bottomed ones of the same variety, that claim may have some merit. However, if it does, it is due to the pepper’s size, not its number of bottom lobes, and the difference would be negligible when it comes to paying for the pepper by weight.
The difference between three bottomed bell peppers and four bottomed bell peppers cannot be found in taste or texture. There may be slight differences in size and in the amount of seeds they produce, but these differences are negligible. The only real difference, which is so slight that many bell pepper eaters are unaware of it, is appearance.