In Chrome, is there a way to search only within my bookmarked sites?

I just released a Google Chrome extension called SearchMark that will do exactly what you want. Hope you find it useful.

You may use the browser-based Historio.us.

This is what makeuseof.com says in Historious Takes Bookmarks To The Next Level:

The idea behind Historious is simple. Instead of storing bookmarks in folders, they’re all individually indexed; just like Google does with the whole of the internet, to create your personalized search world. This search engine, which can be used in every browser, across computers, allows you to search both by title and content of the indexed pages.

Historious works across browsers by bookmarklet. A bookmarklet is a (regular) bookmark that executes a bit of Javascript code. You’ll be able to add it to your bookmarks bar after you’ve completed (free) registration. Alternatively, there’s also a Google Chrome extension. This works exactly the same as the bookmarklet, and nothing keeps you from using the extension on one computer and the bookmarklet on another.

It seems Google has a custom search you can point to your bookmarks file. From their doc, "Here's a quick and easy way to create a search engine from the links on your web page": http://www.google.com/cse/tools/create_onthefly

The way I use it, I have to export my bookmarks from xbel to an .html file, but that's a useful thing to have anyway. (Especially since I haven't found a Chrome equivalent to Galeon's "My Portal").