The lead developer behind the popular Mac dock replacement DragThing and the fantastic iOS scientific calculator app pCalc is about to be sued for patent infringement because his software uses Apple’s own in-app purchasing mechanism. And he’s not alone.

Not only will the lawsuit delay the latest update to the free version of pCalc, pCalc Lite, it may just be the opening shot in an IP war, not just against Apple, but against the devs who dare to sell their software on the App Store.

Developer James Thomson of TLA Systems first broke the news that the latest version of PCalc would be delayed due to the threat of a lawsuit this morning on his Twitter feed.

“Just got hit by very worrying threat of patent infringement lawsuit for using in-app purchase in PCalc Lite. Legal docs arrived via fedex,” Thomson wrote.

“No idea what to do… They seem to be effectively claiming the rights to in-app purchase, but going after me, not Apple.”

Thomson is currently working with Apple as a first step to knowing how to address the issue, but it’s clear Thomson would rather not go to court, although will if he has to. “A decent IP lawyer will burn all the profits from PCalc in-app purchasing in one day,” Thomson notes.

Although Thomson does not want the name of the company who is threatening to sue him on record unless he pays up a hefty licensing fee until he speaks to Apple Legal, he makes a point of mentioning that the lawsuit does not appear to be app-specific.

“As far as I can tell this is not PCalc specific in any form,” Thomson wrote. “It doesn’t seem to be in any way app-specific.”

If true, it seems that someone is taking aim at small developers to try to extort them out of licensing fees for using Apple’s own in-app purchasing mechanism. That’s the nightmare scenario of many small devs, who don’t have the resources to fight off patent trolls.

Worse, it appears that Thomson might not be the only target. Already, other devs are reporting getting hit with lawsuit threats via Fed Ex.

Patrick McCarron, a developer for MobileAge, confirmed that he was also hit with a threatening patent lawsuit over his use of Apple’s in-app purchasing mechanism this morning on Twitter.

“Anyone else get a patent threat via FedEx for in-app purchase use in their iOS app? So far @jamesthomson and I got hit.”

I imagine we’ll hear more reports this morning of other devs getting similar letters. This seems to be a campaign.

With small developers under fire by a mysterious patent troll for using Apple’s in-app purchasing system, it seems likely that Apple itself will step in to smack down the offending company. Even so, this appears like it will be a stressful morning for many developers.

Are you a developer who was hit with a lawsuit threat this morning for using Apple’s in-app purchasing system? We’d love to hear from you, either in the comments or by email.

Update: While we still don’t know who is threatening to sue Thomson over IAP, another company is also suing indie iOS devs over their patents, this time in-app upgrade links. Is this a trend?