Can someone please answer this? I'm wondering this myself.
You have to wait for the jb team to come out with a jb for 4.1. If you update to stock 4.1, you lose your jb. It's no big deal to wait though since the jb usually comes out very quickly after an update from Apple. If you do jb, make sure you use pkgbackup to back up all of your jb apps (it backs them up as a contact in your address book). Once 4.1 comes out and the dev team releases a jb for 4.1, you jb again, install pkgbackup and run a restore from within the program - that will reinstall all of your jb apps, repos, etc. Super easy.