Aside from IOTA not having viable options right now, best practice is to keep your other coins/tokens on hardware wallets (or old fashioned paper). I use a Nano Ledger S and it does the trick. Exodus (a desktop wallet) only supports BTC, Dash, Decred, Ethereum, Golem, Litecoin, and OmiseGo, but they're regularly adjusting their support portfolio with each version release. As long as you're not an active trader, get the bulk of your crypto off exchanges. You'll feel safer as long as you can secure your password and recovery phrases adequately. Exchanges can be hacked, have glitches, or go down completely to lock you out when you might need access most. For exchanges, I recommend 2FA security, which is sometimes optional.