I generally leave them in the deck, but at the front or back so I can take them out easily. I rarely use them in tricks these days, but that's not a conscious decision, I just haven't been doing tricks that specifically use jokers. A lot of what I do involves the colors or suits of the cards, so I take the jokers out because they just muck up the works for that stuff.
I do use them for torn and restored and such, but I've got so many decks of cards just sitting around that I don't really worry about stock piling spare cards any more.