It depends on what you mean by "best." Most secure, or most efficient? Your threat environment usually determines the type of algorithm you need to use (legal and technical restrictions not withstanding), but for most commercial security applications, 3DES, Twofish and AES are usually more than adequate.
If your data transmission is characterized by high speed and small footprint, in a wireless environment, for example, take a look at the NTRU cryptosystem from NTRU (www.ntru.com).
For more information on this topic, visit these other SearchSecurity.com resources:
Ask the Expert: The difficulty of stealing information compressed with a private algorithm
Executive Security Briefing: Public key cryptography: Q&As from your peers
Best Web Links: Encryption
This was first published in May 2002