Tons of blank icons (bookmarks) keep showing up

Did you download any of the blank icon creators like iBlank, etc? If so, I'd say you should uninstall (and reinstall if you want) and go from there. If it continues to be an issue, you may want to just restore and rejailbreak

I've tried the options in Cydia (not sure what they're called anymore) but always ran into issues with them. When I restore, I always take screenshots before, then transfer them over to my computer so I know what I had previously. Then, when I have a few hours to burn, I add everything back. It's time consuming, but it's not like I'm ever all that busy anyways

I had a problem that sounds the same. A little while ago, I installed Clockscreen, and it "came with" 12 blank icons. I could delete the icons, but re-springing would bring them all back. I was thinking about taking apart the .deb file to see where it was hiding the buggers, but ended up manually copying the Clockscreen theme to a temp folder, removing Clockscreen, and moving the theme back. Voila! No more extra icons.