Running Snow Leopard on my Mac Pro 2009.
Pretty straightforward troubleshooting if you want to skip to the end, although how I got to this place might help:
About a month ago I had a massive system crash, the cause of which I cn only attribute to Flash (statistically 80-something percent of crashes come from this little twerp, right?) I could not perform a normal boot, so I looked at Verbose Mode and saw I was getting errors which I cannot quote verbatim leading me to believe I needed to free up space on my hard drive. So I did that in Safe Mode, and it still wouldn't boot in normal mode. I tried again and again and on the 3rd time with no real explanation it booted normally. For a while it would boot and after maybe 3 hours of uptime the Finder would start beachballing my cursor and slowly every app I touched would irreversably freeze. I would force quit Finder (which would never restart) and other things but ultimately everything was frozen except my cursor. The Apple Menu and Cmd+Opt+Esc wouldn't even come up.
I dealt with this for a while and figured I'd bust out TechTool, DiskWarrior for a permissions and directory overhall, and iDefrag (it was insanely fragmented). Well, after polishing my data to perfection I'm back to not being able to boot normally, but I know the disk utilities didn't kill my drive because I can still do a safe boot. Things seem pretty stable in safe mode, so there's a leech somewhere to salt.
So, what are the main differences between a normal boot and a safe boot? Are there some usual suspects I can flush out? Does anyone know how to do a complete purge of Flash's imfluence on my computer?
Should I post my boot logs from the console to help?