This is really a great question, because it's exactly the kind of thing somebody starting out would need to know, but it's very hard to figure out how to ask about or google for.
Unfortunately, to do what you're describing you're going to have to make some concessions somewhere to achieve what you're talking about. Double unfortunately, because I think you're probably going to want to go the route of the web app, unless print quality is the major overriding concern.
For starters, let me point out Mathematica Player and their "open" CDF format. This might do what you need right off the bat, although you're likely to wind up spending big Mathematica money to make it all work out.
What kinds of things are easier with a webpage? Most things:
- Interacting with other users in realtime
- Social nonsense
- Facebook, Twitter, Youtube linking and embedding
- Most kinds of dynamically generated content
- Interactive charts and graphs, e.g. with d3.js
- Interactive 3D visualizations, e.g. with canvas 3D
- Real-time updating—fix a typo, everybody sees the fix as soon as they reload the page
What you'll be giving up by using HTML, essentially, are the following things:
The ability to perfectly control how it looks on somebody's computer.
Different computers and different browsers render the same pages differently. Even the same browser on the same system can be configured differently—replacement fonts, minimum sizes, and user stylesheets can all radically alter the display. You'll just have to accept this if you go HTML and just do the best you can.
The ability to control how it looks printed. There are print CSS rules that enable you to achieve a nice-looking printout, but a lot of the things TeX does for you and well (page numbering, for example) you will lose. The browser will attempt to do these things for you, and will do a bad job. Little direct control over headers and footers.
Fancy TeX algorithms. There's no automatic hyphenation, no TeX justification rules, no hanging punctuation. Math is not automatically rendered well—MathML is much more manual than TeX math.
Any sort of procedural stuff TeX does. No table of context generation. No bibliography management. No automatic footnotes.
To some extent, the ability to have an offline reference.
- MathJax renders TeX math.
- Sweet Justice implements hyphenation.
- Typeset implements the actual TeX justification algorithm.
- Pandoc can convert between various formats, including LaTeX and HTML; some of these plain text formats support some of these features—Markdown supports footnotes, for instance.
- jQuery is frequently used to implement odd/even rules and could easily be employed to implement various procedural effects, though it is a lot more of a general purpose tool than the rest of the items in this list.
It wouldn't be terrifically hard to take these various technologies and create a kind of "TeX template" for the web. At this point, what you'd mainly be missing is style, but mostly book-level features like headers and footers. Of course TeX will still do a better job than these libraries at some of these purposes, because it has better information, is better debugged, and can afford to take the time to do it right, but you can certainly achieve a passable quality (not quite typesetting) and get all the other things you need to do going as well.
I'd expect this will get you closer to where you want to be than banging PDF into shape. But I'm a web developer by trade and do TeX on the side for fun (lately) so I am probably biased.