After being asked that question repeatedly ever since the Mega Man comic series was announced, and a bit of teasing, Archie comics announced yesterday a crossover between their popular Sonic and Mega Man comic lines! The original news from Kotaku are found here, while the official press release is also available.
The crossover, lasting 12 issues, will be written by Ian Flynn. This is the same man who's already taking care of both series and is familiar with both lores down to very specific details, so I'm expecting something great to come out of this!
Source: Kotaku article|Press release