It is possible to encrypt some protocols but not others, in the same tunnel?

Clients have a PPP tunnel over a wireless tunnel to the gateway for authentication and accounting. Currently the tunnel itself is encrypted, but the encryption/decryption process at each end must add latency and absorb router resources. Is is possible just to encrypt, say http, ftp and the mail protocols for privacy while allowing all others which don't really need it but do need speed such as Skype, VoIP and games to pass through unencrypted?

For ppp tunnels it is not possible.

Thanks.