How to keep neutral silicone?
Stick a deck or drywall screw in the hole.  Remove it from the applicator.  

It will harden up.  When ready to use again, yank out the drywall screw. 

Remember silicones have a finite shelf life of only a year, or maybe two if stored in ideal conditions. The worst thing you can possibly do to yourself is try to use a silicone sealant that is too old.  The problem isn't just it failing, but the huge mess of removing all of the faulty product so a new application has a chance!  Silicones are annoyingy hard to remove.  

Because of this I am very shy about reusing old silicones unless I am very sure of their provenance.  It's not worth screwing up your project to save half of $5.