Other than the system extensions (which you normally cannot remove) - this should not cause any problems. Its a good idea to backup the ePO folders and database - in case you anticipate issues.
Also there are a bunch of legacy products that are listed under Policy Catalog drop down which are not really supported. You can get rid of these by using a query like so (make sure you backup the ePO database before doing this):
DELETE FROM EPOSOFTWARE WHERE PRODUCTCODE IN ( 'ALERTMNG4700', 'ALERTMNG4710', 'EPOAGENT2000NVNW', 'LYNXSHLD1300', 'LYNXSHLD1400', 'NSHLDNW_4600', 'OUTMAN__4600', 'SNOWCAP_1000', 'VIRUSCAN6500', 'VIRUSCAN7100', 'GSDOMINO5000', 'GSDOMINO5300' ) Go
Generally speaking ePO won't let you remove extensions with dependencies, or core extensions by accident..
As Sailendra suggests, a DB backup before major changes is alwaysa good idea though !