With a program that runs thousands of lines, it would be helpful if there was some way to have a "Table of Contents" on the side, a listing of the (user defined) "chapters" of the program.
Adobe Acrobat Pro, for example, can pop out a Table of Contents sidebar, where you can navigate to and fro around a book, while still viewing the pages of the book.
I realize it's important to compartmentalize code, though, and not have everything in one massive file. But I'm still on the lookout for some system of TOC/chapters.
Is there something like this out there, besides in-code segmenting, such as commenting various code sections and then expanding/collapsing segments? Not that there's anything wrong with this method; it just still requires scrolling up/down/around the actual file itself, rather than a separate listing.
It doesn't have to strictly be a "Table of Contents" -- it could be some type of code map, overview, or layout -- just a bit of visual overview of the sections/pieces of the program, both for quickly jumping to sections, but also the nice benefit of being able to see an overview of where the program's at so far.
EDIT:
I'm currently focusing my programming in PHP, Python, and Java. Any IDE recommendations for any of these would be helpful -- I'm not necessarily looking for one that will work for all (which I'm guessing some trickery in Visual Studio would be the most likely solution for such).
I find that using regions in Visual Studio I can quickly organize code and find what I'm looking for. With C#, you can nest regions within regions as well.
#region Something Cool
#region Alpha code
#endregion
#region Beta Code
#endregion
#endregion
You didn't make mention of which IDE you're using, but this might be useful for you.