With the advent of integrated email into devices like the iPhone and iPad this is no longer a frequent choice you have to make. But when you occasionally install a new Office suite, or get a new laptop and set it up, you still run across this question. Especially if you want to read your Gmail, Hotmail, and Yahoo mail in your MS Outlook or OS X Mail programs.
The technical details of the choice are no longer relevant. They don’t really matter any more as I have done this dozens of times. My choice should always be IMAP.
Now that I have documented this in my blog, I can always come back to here when I need to remember or research which option to choose. IMAP. IMAP. IMAP.