Basically, if a CVAR already exists and it lets you change it, you'll be fine. Some servers will kick if you change it outside of a certain range, for example /com_maxfps should be between 50 and 125 on many servers, but others allow any range.
A common check is to force LODSCALE to a certain value to keep people from disabling grass...but you can get kicked for that without even touching a CVAR. If you set all your graphic textures to low, you'll get a warning and then a kick if you fail to correct it.
If you want a list of what a server allows, open the full console (shift-tilde) and do a /pb_cvarlist
The only values you would be banned for are ones installed by cheat programs, so as long as you don't have any of those don't worry.