linux "scandisk" equivalent
 

ditto

had some bad blocks while installing-- just wanna make sure everything is ok

Would you be referring to fsck if your wanting to run a scan on your system in Linux ??

what version would I use for ext3? I read some warning about fsck, is there a greater chance of system damage than w/ using windows scandisk, or is it about the same?

There are plenty of warnings about using it with mounted file systems when you start it due to the possibility of another process writing during scanning.
I usually use my boot disk (yes, I actually made one) or the install cd's and "linux rescue" to get a shell.
Then fsck the partition. I won't use the automatic function.