The answer depends on what you are trying to do. If your goal is basically a complete web browser simulation, or a “headless browser,” there are a number of solutions, but none of them (that I know of) exist cleanly in .NET. To mimic a browser, you need a javascript engine and a DOM. You’ve identified a few engines; I’ve found Jurassic to be both the most robust and fastest. The google chrome V8 engine is also very popular; the Neosis Javascript.NET project provides a .NET wrapper for it. It’s not quite pure .NET since you have a non-.NET dependency, but it integrates cleanly and is not much trouble to use.
But as you’ve noted, you still need a DOM. In pure C# there is XBrowser, but it looks a bit stale. There are javascript-based representations of the entire browser DOM like jsdom, too. You could probably run jsdom in Jurassic, giving you a DOM simulation without a browser, all in C# (though likely very slowly!) It would definitely run just fine in V8. If you get outside the .NET realm, there are other better-supported solutions. This question discusses HtmlUnit. Then there’s Selenium for automating actual web browsers.
Also, bear in mind that a lot of the work done around the these tools is for testing. While that doesn’t mean you couldn’t use them for something else, they may not perform or integrate well for any kind of stable use in inline production code. If you are trying to basically do real-time HTML manipulation, then a solution mixing a lot of technologies not that aren’t widely used except for testing might be a poor choice.
If your need is actually HTML manipulation, and it doesn’t really need to use Javascript but you are thinking more about the wealth of such tools available in JS, then I would look at C# tools designed for this purpose. For example HTML Agility Pack, or my own project CsQuery, which is a C# jQuery port.
If you are basically trying to take some code that was written for the client, but run it on a server — e.g. for sophisticated/accelerated web scraping — I’d search around using those terms. For example this question discusses this, with answers including PhantomJS, a headless webkit browser stack, as well as some of the testing tools I have already mentioned. For web scraping, I would imagine you can live without it all being in .NET, and that may be the only reasonable answer anyway.