If a Chinese website or tool is doing a good job, you don't have to spend a lot of time thinking about the difference between Chinese popovers or fixed window lookups. You may prefer fixed windows to popovers (or vice versa), but which is better at proving extra information? Do popovers help Chinese learners understand text more quickly? Do fixed windows help people reading Chinese read more effectively?
Since I create tools for studying Chinese, I think about questions like that all the time. But before I answer those questions, an introduction to the differences might be helpful.
Popovers are commonly used for providing extra information to specific parts of a text. For instance, if you put your mouse above this link to 3000 Hanzi's Chinese-English Dictionary for a few seconds, a message will appear in a yellow box: that's a popover.
Chinese learning tools often use popovers as a dictionary lookup. 3000 Hanzi's dictionary has a popover tool, as do tools like Perakun. If you want to lookup words while you're reading a popover tool might be just what you're looking for.
You may think you haven't used a fixed window tool before, but if you've been using the interwebs for the past 2-3 years or if you've used a computer operating system in the past 20 years, you've encountered fixed windows that, like popovers, are used for providing you with extra information. If your browser has a status bar on the bottom, or if you use a file manager like Explorer or Finder, you are using fixed windows. On browsers, the status bar might provide information about links when you hover over them (in the 90's, people even added scrolling messages to the status bar), and on file managers, it might provide information about how many files are in a directory or even information about a particular file like the file's size.
I first encountered a fixed window in a Chinese learning tool when I used Wenlin's dictionary bar. It was the inspiration for 3000 Hanzi's dictionary bar which is the default for 3000 Hanzi's Chinese Reader. It's also used on sites like nciku.
When creating Reader, I originally had to make a decision between popovers and fixed windows. I chose fixed windows because they are easier to create. With a fixed window, you just need to create one box or window and leave it in a fixed position. Popovers are much harder because each one has to be positioned just right, especially if you want to let users click or select text inside of the popover. Popovers also need to appear and disappear at the right time--they shouldn't hang around too long or fade away too quickly. Creating a good fixed window that users can click and interact with is relatively easy; creating popovers that do the same job isn't.
Unfortunately, being easy to create doesn't necessarily mean it's better for a Chinese learner. When it comes to usage, popovers do have some distinct advantages over fixed windows. First, popovers are closer to the action. You can't avoid seeing a popover. That's why they are so useful (or, occasionally, so annoying). Popovers make clicking buttons to play sounds or view more information really easy for the learner. Popovers are more active.
Fixed windows tend to be more passive. If you don't know about the fixed window, you might not even notice the information changing inside the window. But once you know it exists, it's really easy to locate and it doesn't distract. 3000 Hanzi's Chinese dictionary bar also has buttons for sounds and adding words to vocab lists, but sometimes, the bar is halfway across the page. If you wanted to add a lot of words to a list, using the dictionary bar might get a bit tedious.
Solutions for different problems
So the real answer to the question, which is better: Chinese popover tools or Chinese fixed window lookups, is: it depends. They excel in different areas. Popovers are great for studying because when you're studying, you're actively looking up lots of words and saving them to study later. But fixed windows are better for reading because they offer less distraction and are less of a crutch.
That's why 3000 Hanzi has both a Chinese popover tool (which is the default choice on dictionary searches and on pages like the Chinese measure words page), and a Chinese Dictionary Bar (which is the default choice when using reader). Letting Chinese learners switch between the two is just gravy.