I have two questions about my Kindle 3rd Gen (Latest):
1. Is there a "back?" After performing a search at the Kindle store, I sometimes inadvertently hit the "Back" button losing my search results and forcing me to retype in my search terms. Is there anyway to move "forward" to the search results I just lost? For example is there an alt-key combo that takes me forward instead of just back?
If you're in the browser there is a left and right arrow at the top left of the screen that works like 'back' and 'forward' on a regular browser. But, no I think there's no way to go back to where you want back from.

2. Search terms? I recently purchased a wine encyclopedia with over 700 pages and thousands of entries. It has been indexed. Since the encyclopedia is in alphabetical order with sections for each letter, I thought I might be able to navigate the publication by letter. No. I have to either perform a search or jump to a page. Not convenient! I just wanted to jump to a particular entry for "fortified wine," like I would in a real world book.
Furthermore, when I searched on a term, in this case "fortified wine," the results page brought up over 80 results where the term fortified wine is cited within the publication. That's a LOT of results to wade through just to find the entry entitled "fortified wine." Since citation "relevance" is not included in results that I can tell, it can take a long time to find what I'm looking for. Therefore:
Is the index indexed for Kindle . . .meaning active links in the index entries? In that case if you went to the index, it would have links to the entries, but you'd still maybe have to browse. To search, you can, from anywhere in the book, just start typing the thing you're looking for. In your example, I'd search on "fortified"; type it in and then click the 'find' which will tell it to search in the book only. It should find everywhere that word is in the book. I think if you search for 'fortified wine' it will show all instances of fortified AND wine. . .as it is the search doesn't allow and/or searches unfortunately.
a. Can I search a publication by chapter title? (in this case I would search for the chapter "F" for fortified wine)
If the chapters are actively linked you can just use the Table of Contents. But, yes, searching for "Chapter" should bring up all of them and then you can skim through for "Fortified Wine". Then I'd suggest you bookmark that chapter if it's something you'll go to often. Don't just search for "F" as there will be a lot of them in the book, no doubt.

b. Can I search an encyclopedia by entry title by using special search terms such as "@definition" or some such thing?
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Don't know the answer to this. . .but I suspect not. I think searching that way will give you everywhere the word 'definition' appears, or maybe nothing as "@definition" is not a string that appears at all. But I might be wrong -- there's a niggling in my brain about using the @ but I can't recall how it works. . . .
If there is no way to search by special terms, I thought of annotating or indexing the book myself. Not sure how hard that would be. So I'd annotate the "A" section's first page. Then I'd do the same with the "B" section's first page, and so on. Any tips on that?
You could bookmark relevant sections. You could also place notes or highlights in relevant sections. . .I think they can be searched on as well. Before 'collections' many folks used a sort of tagging system to organize their books. They'd use unique search terms like qfiction or xmystery so that there would be limited occurrences of the 'tag' word. Maybe something like that would work within a book as well. You'd add the tags as a note at the appropriate place.