Blockade runners will lose their agility and warp strength bonuses, becoming ships geared more towards stealth. They will be able to fit covert ops cloaking devices, and thus will be able to warp while cloaked (and warp faster than many standard ships, if warp speed remains unchanged from current stats). In its new role as a stealth-based ship, blockade runners will also be able to use black ops jump portals, (in theory) allowing pilots to evade heavily camped gates altogether.
While blockade runners are losing their warp strength bonus, deep space transports are inheriting them. In addition, their active tanks are being replaced by bonuses that are geared towards a hitpoint tank, meaning that bonuses will be imparted to shield extenders and armor plates .
CCP Chronotis also spelled out the changes coming to EVE's mining ships -- namely, the Mackinaw, Procurer, Skiff, and Rorqual. The Mackinaw will receive increased CPU and cargo capacity, putting it on more equal footing with the Hulk. The Procurer and Skiff will receive agility bonuses, which Chronotis hopes will "nudge them towards more of a ninja mining role." He also dropped a bit of a surprise: The Skiff has always had a hidden bonus, a +2 warp strength that was never listed in the ship's description. That bonus will remain, and will now be listed. Lastly, the Rorqual will get a slightly increased corp hangar capacity, improving the ship's ability to house the output from mining ops.
These changes outlined above are still only proposed changes, and CCP is currently seeking input from players as they move forward. Chronotis also stated that there may well be more changes in store for these ships, such as specialized cargoholds, but for the time being the listed changes are what they're currently focusing on. Players are weighing in on this dev blog, Rollin' Rollin' Rollin', and what the proposed changes could mean in a related thread on the official forums.