FanComics? Well, yeah, they've been around for a long time as can be seen from "2001 BC: A Spam Oddesy" and "Don't Spok The Afflicted" - hold-overs from the days of hard-copy fanzines which can be seen online. As with other media, modern technology - computers and the internet - have given the masses the tools and a distribution medium to really develop on this.
There are a lot of "one-shot" webcomics online such as K'Pinky and the Brain and Worst Wing as well as the vast "Sev Trek", although it isn't all free now. Some prospered for a while and then folded, like the superlative "Enterprise Oddities" and Trek Wars, which seems to have ground to a halt half-way through chapter 3. "Star Trek: Phoenix-X" hasn't posted an update since November, but the pace of production there is pretty casual so it need not be in hiatus."STS: The Forgotten Frontier" is still going strong though, it's up to issue 365! Is that some kind of a milestone - a year of posts?
One long-running favourite is still cranking out issues, albeit at a very modest rate! Kail Tescar of TAS Comics has eight issue available for download, not including a special featuring the characters from "Starship Exeter". At the moment, he has several comics scripted and is working on their artwork but he could use some help creating aliens. If you like the Animated Series style,and you have some artistic talent, contact Kail on email@example.com.
New comics are springing up to take the place of the older ones, for example the USS Tamarlane that has just published it's first issue plus "ST: TNG - Damaged" by Aric, which it was my privilege to help promote during the Twelve Trek days of Christmas.
April '07 saw the start of "TOSS" by Leckford, a below decks look at the daily life on a non-canon ship he has designed called the USS Mumbai. Interestingly, Leckford also has a second comic called "Percy Street" whose protagonists are making a Star trek fan film! Be warned though: it is sexually explicit in parts although I thought it was well handled.
In some cases a die-hard fan has to keep a sense of proportion and allow Star Trek to be lampooned but in all cases we can see how much of an impression the franchise has had on the public psyche. Expect to hear more about Star Trek webcomics in the future.