There's a code you can use to make the text different colors.
Step 1: Hit enter (it doesn't matter if you're in /g or /s or /w, the code will show only in the GMotD if you do it right) OR go into your macros and start a new one. I use a macro, as shown on the right in the image above, because I don't have to remember the color codes every time.
Step 2: Code. (You may copy-paste mine, if you like.)
/run GuildSetMOTD("\124Cff001EFFThe text you want to type for the guild message. ^_^\r\124CffFFF200More text with a different color and a line break.")
It'll come out like this:
Guild Message of the Day:The text you want to type for the guild message. ^_^The line break is the \r. The color code is \124Cff______. Insert a color code into that blank and it'll turn out just dandy.
More text with a different color and a line break.
If you do it in a macro, you can just change the text every day. The only real drawback is that this code defaults back to whatever the guild message of the day was in the panel before you changed it when everyone in the guild logs off.