The newest version of Evernote finally has a highIight tool!!! but I'll leave this up in case anybody still wants to use these other methods or you're still on an older version.
If you've used Evernote for more than a minute you've probably noticed there's no highlight tool. I'm not going to get into how ridiculous this is for a notetaking application, but instead I'll show you the different ways you can highlight. Some are more useful than others depending on what you're doing. I'll be focusing on highlighting Wikipedia articles because that's what I needed to highlight and clip.
I'll be using Firefox and the Windows Evernote client but I'm sure that most of these will work on other browsers and systems.
1 - "Highlight" Change Text Color
2 - Evernote Clearly
3 - ENML
4 - PrintScreen
5 - Highlight on Pages with Firefox Addon than Send to Evernote (psst, the best option...)
5 1/2 - Copy/Paste Highlighted Character (Blank Space with Highlighted HTML)
If anybody knows any other methods, or alternatives for other OS's and browsers, please tell me and I'll add them to the list. There's plenty of articles on how to do this out there, but none that explain all the methods, hence this instructable.
Step 1: "Highlight" Change Text Color
Step 2: Evernote Clearly
Click that icon with the little letter T or by hitting Ctrl + Alt + H. You can change the shortcut by going to Firefox > Add-ons > Clearly (Options) > Options
The downside to this is that unlike the Web Clipper it doesn't have the option to sync through your desktop client, therefore using up some of your monthly allowance. This won't work for you if you plan to merge notes, or organize the clipped text, and therefore use up even more of your allowance.
Also the highlight color is not quite yellow (this can't be changed) and you can't keep a website's formatting. It clips the formatting from the clearly theme you use. If you hit Ctrl+Space in Evernote it will format it to your preferred font and font size (you can set this in Tools > Options > Note) and make the yellow a brighter yellow.... BUT the moment you leave that note, the highlighting will disappear. When you go back to it nothing will be highlighted.
Step 3: ENML
To explain what ENML is, here's a quote from their site.
"Evernote has a nice WYSIWYG editor on most of its platforms and it works for normal people. But some geeks want more: If you can read and write XHTML and you are not afraid of potentially screwing up your note, use this webapp to edit the underlying XML content of a note. And since the XML content must comply to the Evernote Markup Language ENML, this webapp is called ENML Editor."
So you can do a lot more than highlighting, but I'll focus on that.
First you connect your account. The steps are pretty simple. Your note has to be made already and synced (which is a HUGE downside). You copy the note link, paste it, and open up the editor.
To highlight something, copy <span style="x-evernote: highlighted; background-color: #f6ee96"> in front of it (you can change the color to whatever you want) and </span> to the end. Yeah, not fun... But if you want to edit a lot of things it might be useful (background color, etc.) They offer a bookmarklet on their page if you don't want to have to do the same three steps over and over.
Step 4: PrintScreen
You could also just highlight with your mouse courser like you're selecting something and PrintScreen that if you want to be faster.
The downsides to this are just about everything. Don't worry, I'm getting to the best method.
Step 5: Highlight on Pages with Firefox Addon than Send to Evernote
Then select what you want clipped and send it to Evernote with the Web Clipper (which allows for online AND offline clipping). Unfortunately simplifying the formatting doesn't work but you can change the font and size and the highlighting usually looks find (adjusts it's size, etc) unlike with some other methods. Also some text might simplify itself as you see in the second picture if you clip from a selection (not if you clip from article view or fullpage). Copying it to a note by hand will simplify even more formatting (like the word "Wikipedia").
The downside to this method is that it leaves some spaces highlighted sometimes between changes in formatting (links, underlines, etc). You can fix these by backspacing the blank space than adding a normal space. It's tedious though so... you might want to get used to the spaces. Most sites aren't as formatted as wikipedia, so it might not bother you anyways.
Article View | Selection Clipped | Selection Copied by Hand | Original Text on Wikipedia (well not quite so original as I have a few add-ons for it), but you can see the lack of blank spaces.
Step 6: Copy/Paste Highlighted Character (Blank Space with Highlighted HTML)
If you're typing up something up and wish to highlight as you go copy a space in a highlighted text (from Word, from some text you highlighted with an add-on, etc), some might work better than others. Some might blank out when you leave a note. I think all will loose their highlights if simplified, but some can have their font changed without the highlights being too short.
If you don't understand what I'm saying about copying a space, just copy the gray area between two words like I selected above.
Now paste this anywhere you want to write in highlighted text. I suggest you paste it at the top of your note temporarily if you will be copying and pasting other things. To stop writing highlighted just copy a non highlighted space.
You can also paste text right after a highlighted space to make the entire pasted text highlighted. You have to "Paste as Text" though, normal pasting doesn't work.