Seeing as how Googling iPhone -Apple -Cisco
returns around 2 million results, I think it's safe to say that Cisco won't likely win a court battle.
Having a registered trademark isn't like a patent: you have to actively enforce trademarks in order to protect them, which they clearly haven't with any iPhone other than Apple's.
Further hurting their case is that trademark law is almost exclusively focused on protecting the consumer. In other words, trademark violations are only problematic in-so-far as a consumer would genuinely be confused. Therefore, even though Apple just announced the iPhone, since people were openly calling their phone the iPhone for months (years?), they likely have a stronger claim to the name. Instances like whatever blog it was that preannounced Cisco's iPhone as "the iPhone," where people assumed it would be the Apple iPhone, likely play to Apple's favor. The part where they had to emphasize that they did, in fact, own the trademark, also don't help.
Of course I'm no expert at law, though :P I'd be interested in shawnj's or melgross' opinions.