From an archaeological perspective, wells represent or can represent nifty time capsules of sorts as they are often a fairly well protected and quickly buried environment. Relatively quick burial and anaerobic environment kept fairly constant, such as kept wet meant it was a stable environment largely free of many of the chemical and biological threats that would ruin items simply recovered subsurface that get wet, dry out, get wet, dry out, freeze, thaw, freeze, thaw, etc.
If the pistol was found in the well as reported, it likely was not "lost" in the well as that would have been an unusual place to lose such as item. It is noted here,
http://www.ocregister.com/ocregister/healthscience/scienceenvironment/article_1223231.php that the pistol could have been lost by somebody who put it down next to the well while getting a drink and it got knocked in, but you have to realize that the well was hand dug, not very deep, only about 12-15 feet, and an item of such value and rarity in the new world would have been retrieved had the owner known he (probably 'he') put it next to the well and it got knocked in by accident. Notice in the article here that the archaeologists were digging through trash in the well. So the well was used as a trash pit. Also note that a halberd and serveral other items were found inside as well, largely intact. These were not "lost" items that just were dropped in by accident, but instead were likely intentionally deposited there for whatever reason, potentially as items that could not be taken with the colonists when they "left" Jamestown or were put there to keep them from falling into the hands of the Native Americans...much like was supposedly done with some of the weaponry at the Alamo.
Excavations of wells can provide very interesting and well preserved materials as can excavations of privies. In both cases, confined and below ground excavations can be very dangerous due to wall collapse and gasses such as methane and carbon dioxide.