Most likely to cause crashes due to being overwritten.
STA $xxxx

Why this specifically? Register addresses like $2100 (Screen Display Register) are stored to this way.
Pretty much all the registers are generally a bad idea to overwrite.
For the most basic protection against ruining these is to look for STA $xxxx / STA $xxxx,x / STA $xxxx,y and whether or not any of the registers are being written to.

Also remember that STA $4200 would translate to XX 00 42 due to endianess.

http://wiki.superfamicom.org/snes/show/Registers

Some complicated stuff like STA ($xx) or STA [$xx] may be an issue but you probably won't be able to tell if those write to registers so you may as well handle them separately.

The following are also capable of directly overwriting values in ram addresses:

Every other STA.
TSB
TRB
ASL $xx (ASL A is completely safe to change as it doesn't specifically change the value of a ram address -- only the accumulator)
LSR
ROR
ROL
MVP
MVN

But are more likely to be safe to overwrite and should be its own option.