Having just finally finished preparing my taxes to send to my accountant, I thought I'd impart a bit of advice to those of you who are serious about trying to make money from their webcomic.
The first and most important is too KEEP GOOD RECORDS. I did okay with this my first year of going legit business-like, but this past year... well, let's just say that itemizing was a nightmare. Make sure you keep all of your receipts and invoices in one spot, and keep them organized. Every month or so you should go through the receipts and invoices up until that point and enter them into a spreadsheet (break them down into categories such as "Travel", "Supplies", "Business Dining", etc.). Do the same with the income you've earned up until that point. Then, by the time tax time comes around, you're good to go and won't do what I did, which is rummaging through a pile of receipts, scratching my head at the ones that had faded and I had forgotten to label, and wishing I was dead.
The second bit of advice is to get yourself a good accountant. I'm lucky enough to have an entertainment accountant that I met out in LA who is willing to our stuff. This is important because he understands what artists can and can't write-off on their taxes. Sure, you could probably do your own taxes and not have to pay a hefty accountant's fee, but... I've seen those forms and I think the fee is well worth it. Just my opinion.
Also, on that subject, be aware of what you can write off on your taxes. You'd be surprised at the receipts you've just tossed away without thinking about it. You probably realize that when you buy art supplies you can write those off; that's a given. But did you realize that if you go to convention and buy books or comics from another artist that you can write that off as research? Or if you go out for drinks with other artists that you can write that off as networking? If you are paying for something that is connected to your profession as a webcomic writer/artist, chances are it can be written off. But again, it's best to have a knowledgeable accountant who can confirm that for you.
The last bit of advice is make sure you know about the tax laws of your state and any states that you attend conventions in. California is great because you can get yourself a temporary seller's permit for conventions, and you're only obligated to declare your income in that instance. But I know in order to attend ConnectiCon in Connecticut, I had to purchase a full-on permit (good for 5 years), and I'm obligated to declare income quarterly. So make sure you know what's what wherever you plan on peddling your wares.
I'm sure others can chime in with their advice, but this is the stuff comes immediately to my mind.