As an opening note, I want to remark that I think time you enjoyed wasting is never truly wasted, so the bad uses are also good uses whenever you needn’t be doing something else at the moment.
Furthermore, most of the sites I know well enough are not of the business-like kind, so I suppose most of the entries in this post will be marginally on-topic.
Service name: Wikipedia
Productive usage: Obviously, it provides a heckload of information about a fair portion of everything. It’s great for looking up facts, unicode symbols and translations (you can look up the English article and then be linked to the target language Wikipedia’s page about the same subject, provided there is one).
Harmful usage: It’s an encyclopaedia. It’s full of encyclopaedia articles. Including articles about your favourite film, TV show, video game, et cetera. Procrastination risk: Moderate.
Ways to overcome productivity loss: Stay focused and pragmatic. Don’t open links into a new tab.
Service name: TV Tropes
Productive usage: It’s great reference material if you’re writing a story; every writer should know the basics of TV Tropes. It’s also a lot of fun to read.
Harmful usage: TV Tropes is pretty much the Charybdis of the internet; a notorious time sink that sucks in unsuspecting travellers and eats all their time. High risk of tabsplosions.
Ways to overcome productivity loss: No known treatment. Avoid at all costs when on a deadline. Check suspicious links for containing “tvtropes.org”.
Service name: DeviantART
Productive usage: There are lots of tutorials to be found, about things like drawing, photo editing, writing and creating flashes. It’s a fine place to store and present your artwork and/or writings if you have any. There are people there who make the most amazing things; it’s good for finding creative ideas, and it’s good for humbling your artistic self-esteem down a notch.
Harmful usage: I suppose it can be addictive if you really like artwork or writing, but I’ve never ended up trapped procrastinating there. I think it’s fairly safe.
Service name: Omegle
Productive usage: It’s not a place for work, but you can meet all sorts of interesting people and expand your knowledge of the rest of the world. It also has a way of abruptly changing your mood, which can be useful.
Harmful usage: A fairly addictive time-sink at times. It’s part of the casual mainstream internet, and it’s anonymous, so count on meeting a lot of jerks and obnoxious teenagers of the lolcat-reposting type. Don’t go there when you’re bored; you’re liable to spend a long time looking for something to end the boredom without success, boring everyone else in the process. Enter the video chat section at your own risk.
Ways to overcome productivity loss: Just stop reconnecting and go the heck away.