|Disabling system restore before running a virus scan and general nasties cleaning out etc., and then rebooting (after scan completed etc.) means that if anything nasty is found and cleared... it won't be "restored" by system restore. Safe-mode scanning is usually considered/preferable too - again with system restore diasbled.|
Also if anything is found and quarantined... delete the quarantined files - before reboooting and then re-enabling system restore.. Otherwise there's always the chance that a given nasty will escape from quarantine and the rest is history all over again?
Personally I reboot twice before re-enabling system restore.
Also if you go safe-mode etc. with networking and go on-line... you can run a freebie on-line scan too. (Trend housecall is my favourite there.) It can sometimes be that a given virus util doesn't find everything at any given time; may miss what another finds and visa-versa... Thus a freebie on-line and your own local util is a good combination?
Others will occasionally use a Linux CD (Knoppix/Uuntu?) to go on-line etc... This approach allows everything to be checked and again system restore will not be involved in anyway...
If you decide to run any form of registry cleaner... First back up (as in copy to optical-media etc.) "all those important files etc. you wouldn't wish to lose access to... There are accounts of folks finding a registry-cleaner "fixing" things so they couldn't boot up again/log-in etc... Were that to happen and if your files were elsewhere, at least they are safe; and recovery/repair of the OS etc. can go ahead with less concern about losing data?