So I know we never finish these lists, but oh well.
100 webcomics! Preferably write a little bit about each recommendation, and I'll try and update the OP with such.
I'm also going to put in the rule that these need to be comics that one can reasonably read - that is, they have some level of plot rather than being individual snapshots or observations. Which counts out a lot of fantastic stuff like xkcd or the Oatmeal, but it does mean some level of comparison can actually be given.
I'll get started, and prove I read too many of these things...
1. The Order of the Stick
Possibly the greatest masterpiece of gaming comedy, OOTS follows a band of adventurers in their battle against an evil lich for the future of the world. It is witty, genuinely funny, but also capable of providing genuine and powerful characterisation and development in its heroes and villains alike. Non D&D players may find odd panels slow going with the various class and stat jokes that occur, but these will generally become clearer as the work unfolds and moves from a commentary on a game to a commentary on gaming - and, increasingly, to a commentary on ourselves. Somehow managing to move between repeatedly classy punchline gags and heartbreaking moments of bittersweet humour, The Order of the Stick is for my money one of the most enjoyable ways to spend time on the web, and something I'd recommend to almost anyone.
2. Digger
Relatively short by the standards of many webcomics, Digger is a small but exquisite gem of a work. Providing in wombat form a down to earth (pun somewhat intended), intelligent, stubborn, kind heroine, its pages unfurl a story that has a great deal of subtlety and sensitivity whilst also providing heartwarming and whimsical moments. Weirdly, the vampire vegetables turned out to have a basis in actual mythology... in any case, this is a very deserving candidate for the list. Funny and kind-hearted to its core, Digger was a real joy to read.
3. Homestuck
Where Digger pulls you in with a short, powerful, and neatly crafted story, Homestuck does the opposite - engulfing the reader with the complexity, insanity, and breathtaking scale of its plot. What starts out with four kids playing a computer game ends up in a bizarre but brilliantly constructed madness - time travel, multiple universes and realities, and the continual interaction between the strange rules of the game and the reality experienced by the players are all key features. Homestuck swings between soap opera in space, epic duel for world/universe/multiverse/we're not quite sure domination, rules lawyering a game bigger than creation, and hilarious running jokes.
4. Gunnerkrigg Court
Gunnerkrigg Court is the story of a girl at an unusual school that nobody else knows about where odd stuff happens. Which may sound very cliche - but cliches can get that way for a reason, and if you needed a reason for that one Tom Siddell's masterpiece should be it. Skilful and very human storytelling follows the characters and development of the mostly teenage cast with a needle-sharp interpretation of their thoughts and feelings whilst interweaving complex plots around them. The mix of science and myth gives the setting a unique feeling, with references to folk music, alchemy, world mythology, and modern science all pulling together into an elegant and compelling story. Also, the minotaur is called Basil.
5. The Phoenix Requiem
Sarah Ellerton's
Phoenix Requiem is one of the best examples of gothic fantasy in comic form. The sense of suspense and mystery is effortlessly continued throughout the work, with no need for gratuitous scare, gore, or horror tactics. The small but detailed cast of characters are complex and exciting to watch as the plot draws them on and in to the story, which centres around the arrival of a mysterious stranger in a pseudo-Victorian village - and, shortly thereafter, a plague the like of which has not been seen before...