Secure Options for storing Openssl password on a server  (Linux, Python, CherryPy)
For the sake of privacy for a user and other reasons passwords are generally not stored by servers. Typically users choose a password which is stored as a hash of some sort on the server. 
Users then authenticate with the web application by checking the stored hash against a hash supplied based on user input. Once the client is authenticated a session identifier is provided allowing use of server resource(s). During this time a user can for instance upload the file. Encryption of the file on the server should be un-necessary assuming the hosting server is secured properly and and absent of other issues.
In this case, the authentication mechanism is not made clear, neither are the threats that pose a danger, or the life cycle of that uploaded file.
It seems that a server is receiving an encrypted file, plus some type of password. Is the protection of the password being considered during the transmission phase, or as storage on the server? The HTTPS protocol can help guard against threats concerning the transmission of the file/data. As I see from your description the concern seems to be storage on the server side.
Encrypting the passwords once they have been received by the server (either individually or by using a master password) adds another layer of security, but this approach is not without fault as the passphrase either (1) needs to be stored on the server in cleartext for accessing the files (2) or needs to be entered manually by an administrator when needed as part of any processing requiring the password - note that any resources encrypted with the password become un-useable to users. 
While I am not completely aware of what is going on, the most secure thing to do would be to re-work the web application and carefully think through the design and its requirements.
I've implemented a HTTP server (CherryPy and Python) that receives an encrypted file from a client (Android). I'm using OpenSSL to decrypt the uploaded file. Currently I'm using openssl -enc -pass file:password.txt -in encryptedfile -out decryptedfile to perform to decryption on the server side. As you can see the password used by openssl is stored in a plain text file (password.txt). 
Is there a more secure way to store this OpenSSL password? 
Thanks.