In general, I would say transmuting Arcanit Bars is well worth your trouble. Not only will your Guildmates need it, but others will need it too. The key to making money with Arcanite is to watch prices at the AH. Arcane can sometimes go for as little as 20g, which if you sell it at 30g, you are making 10g profit! Thorium is relatively cheap at 8g for 20, it's practically a steal.
You need to check relative pricing at the AH as well. Check Arcanite prices. They usually fluctuate between 30-50g a piece. I've sold an Arc Bar for 50g on a few occasions. Profit-wise they are the easiest 5-10g you can make. My advice is not to take the 5g others offer you, since you will likely make MORE money.
I transmute for guildies for free, and only ask for a small donation if necessary. I've gotten over 300g from selling arc bars alone, so I'd say it's worth it. As with everything, you need to watch the market and strike while prices are high.
Unfortunately, I have an epic quest for a hat that requires Arcane Crystals, so I will have to same those for now, but I guarantee, I will be transmuting when I finish that quest!