What are the bumpy parts around the spindle of some pedals?
The 'official' tool that engages with that bumpy collar is the Shimano TL-PD-40 bearing shaft removal tool. It's a plastic tool designed to be used with a larger wrench, or a vice. Here's a pic: 
TL-PD-40

If you're interested in servicing your pedals using this tool and others, here's a how-to from Park Tool: http://www.parktool.com/blog/repair-help/spd-pedal-overhaul