This is the instruction manual for the javascript viewer. I think the basic functionality is pretty self-explanatory, but there are a few obscure things you can do to help refine your query that require explanation.
"Food Groups" and "Column Groups": These are just simple radio boxes. Click on "veggies" and poof! you see a bunch of veggies. The meaning of the half-full check boxes is explained below, but you probably haven't seen any yet. (I have deliberately made it difficult to select all food and column groups at the same time -- even Mozilla has trouble with drawing the whole database in one shot, I cringe to think what Internet Exploder would do with it.)
"Preparations": This is another panel of check boxes. You can check as many of these as you like. It will redraw the table after each change. (This overrides individually-checked foods -- see below.)
"Data Values": You have the choice of several different ways of presenting the data. "Standard units" is just straight mg, IU, or whatever, and "percentage of USRDA" is equally self-explanatory. "Ranking in list" just displays the ranking (ie. #1 to #N, where N is the number of foods being displayed in the current view). Lastly, "location in distribution" displays how many sigma it is away from the mean. That is, 0 means it is dead-average in the list of foods currently being displayed, 1 means it is a "one sigma" event -- it is better than 67% of the foods being displayed, and -1 means it is worse than 67%. (You could probably make a good argument for using a Poisson or similar distribution for the vitamins and minerals, but I'm too lazy to do that.)
By default it displays nutritional content per 100g of food, but if you check "adjust for serving size" it will display the content per apple, per cup of packed spinach, or whatever, instead. This is extremely useful for making comparisons between different fruits or vegetables, and between raw and cooked preparations of the same food. (See these notes for a lengthy discussion of the difficult technical issues involved in comparisons.)
"Clear and set all boxes below": These buttons refer to the individual check boxes beside the food and column labels in the data table. They do exactly what they say -- they're just shortcuts for checking or unchecking all the darned boxes one by one.
"Redraw table": Just what it says. You need to use this button after certain changes to make them take effect (such as after changing the individual food or column boxes in the table).
"Reset options": This is a useful bale-out option after hopelessly screwing up the settings. It clears everything and starts over displaying vitamin content of raw vegetables.
"Search for food": Type in all or part of the common name of a food, then click on the "go" button. It will ignore all radio box settings and display everything matching your search string. Press "redraw" to restore the previous view. For example, try searching for "soy": you should see an oil, a dairy, and several bean entries.
"Clear search": One or two other controls will also clear the last search, but if you don't want to change anything and just want to go back to where you were before the search, then click this instead.
Food and column boxes: These are the most obscure features. In any given view you are allowed to check or uncheck as many of the little boxes next to the food or column labels as you like. When you redraw the table it will always display any foods or columns you've checked this way. The standard method is to click on "veggies", then check the boxes of a subset of veggies you'd like to compare, then click on "veggies" again to clear it. Now it will only display the veggies you've chosen. The same works for columns. If you want to compare foods from multiple food groups, or columns from multiple column groups, just check the desired foods / columns from each "page" one group at a time, then uncheck the last group to show just the ones you've selected.
The search tool comes in handy when selecting foods across multiple food groups. Note that the radio boxes in "Food Groups" and "Column Groups" will show up as half full when one or more individual foods / columns have been checked this way. The easiest way to deselect all foods and columns is via the "Reset options" button.
Sorting: This is really easy: just click on the column you want to sort on. Click on it again to reverse the sort. By default it sorts by food name. Note the cute little arrows that tell you which column is being sorted on currently.
Food Popup: When you move the mouse over a food label a popup box will provide a little extra info. It includes the quantity of food being measured: either 100g or whatever the serving size is if the "adjust for serving size" box is checked. It also includes the scientific name if available (the USDA database didn't provide scientific names for animals). These are linked to my supermarket flora wherever it overlaps. (This cute little page gives botanical and historical info on the plant or mushroom.)
Column Popup: When you move the mouse over a column label a popup box will provide a little extra info, including the full column label, the units, and the USRDA (where available).