MD5 is generally considered insecure if hash collisions are a major concern. SHA1 is likewise no longer considered acceptable by the US government. There is was a competition under way to find a replacement hash algorithm, but the recommendation at the moment is to use the SHA2 family - SHA-256, SHA-384 or SHA-512. [Update: 2012-10-02 NIST has chosen SHA-3 to be the algorithm Keccak.]
You can try to create your own hash — it would probably not be as good as MD5, and 'security through obscurity' is likewise not advisable.
If you want security, hash with multiple hash algorithms. Being able to simultaneously create files that have hash collisions using a number of algorithms is excessively improbable. [And, in the light of comments, let me make it clear: I mean publish both the SHA-256 and the Whirlpool values for the file — not combining hash algorithms to create a single value, but using separate algorithms to create separate values. Generally, a corrupted file will fail to match any of the algorithms; if, perchance, someone has managed to create a collision value using one algorithm, the chance of also producing a second collision in one of the other algorithms is negligible.]
The Public TimeStamp uses an array of algorithms. See, for example, sqlcmd-86.00.tgz for an illustration.