Most companies that are threatened over patent infringement probably prefer to keep the matter quiet. Therefore the current direct impact of patents on the software industry is not fully known. The following examples probably heavily understate the true effect.
The biggest news at Comdex this year was the announcement of the Compton's patent. Compton's, a spin off of Encyclopedia Britannica, claim their patent covers multimedia searching. Their announcement received a very hostile response from the press. Compton's had been threatening everyone in the industry with a 3% license fee before the Patent Office spontaneously decided to re-examine the patent. This decision must have been a result of all the media attention the patent was receiving. Other than that, there was nothing particularly unusual about this patent. Hundreds more equally broad software patents currently lie dormant in the Patent Office.
Lotus, Microsoft, and Ashton-Tate have all been sued by Refac, a litigation company, for a patent it acquired, #4,398,249, that contains a very broad claim covering "natural order recalculation" used in spreadsheets. Fortunately the case got thrown out on a legal technicality. The patent in question was filed in 1970, but wasn't issued by the Patent Office until 1983.
Paul Heckel has threatened Apple and IBM over patent #4,736,308 which he alleges is infringed by HyperCard and ToolBook respectively.
Cadtrak has collected large sums of money and successfully defended patent #4,197,590 on the concept of an "xor cursor".
XyQuest was forced to remove features from the latest release of the XyWrite word processor after being threatened by Productivity Software. Attempts to license the features proved unsuccessful as Productivity Software increased the fees every time XyQuest attempted to reach agreement.
Mark Williams Company has harassed various software companies over patent #4,956,809 on the (very fundamental) idea of a host independent network byte ordering.
AT&T is finding itself free to start exercising its muscle. It first threatened members of the MIT X consortium alleging that the X11 windowing system was in violation of patent #4,555,775 which it holds on the concept of backing store. AT&T is now suing MCI for alleged software patent infringement.
Novell is being sued for $220 million dollars by Roger Billings for infringing his patent #4,714,989 on the concept of a file server.
The fields of cryptography and data compression are essentially off limits to programmers on account of patents. Numerous companies have been forced to obtain licenses from Public Key Partners, which in turn purchased key patents from Stanford and MIT to create an outright monopoly on public key cryptography. Unisys has threatened people over a data compression algorithm that is also used in the popular Unix "compress" program.
Microsoft is being sued by Stac Electronics as a result of Microsoft's incorporation of transparent data compression in MSDOS 6.0. The main patent involved is #5,049,881.