Here are the benefits of each:
isCOBOL JISAM
isCOBOL APS is supplied with a typical ISAM filesystem, standard in any COBOL application, called isCOBOL JISAM.
Written entirely in Java so runs anywhere, even a mobile phone.
Utility provided for basic file management
Utility provided for one-step migration of data files from Vision.
Maximum file size: 9+ exabytes (EB) (over 9 million terabytes)
Maximum number of keys: no limit
Maximum number of records: no limit
Maximum key length: 256 bytes
Maximum number of segments per key: 16
Maximum record length: 2 GB
Note that isCOBOL JISAM v1 (isCOBOL 2009 SP1 and older) allows a maximum file size of 2GB, maximum number of segments per key of 8, and maximum record length of 32,767 bytes.
isCOBOL ISAM Server
isCOBOL ISAM Server is available for high capacity, scalable, transactional, client/server indexed file data access.
Written in C/C++, available on Windows, aix4, aix5-32, aix5-64, hpux, linux, macosx, sco, soli386, solsparc-32
Includes Client/Server
Full Transaction Support
ODBC Driver for Windows
Supports Live Backup
Memory file support
Includes several feature-rich management utilities
Utility provided for one-step migration of data files from Vision.
Maximum file size: 16,000,000 terabytes (16 Exabytes)
Maximum number of keys: no limit
Maximum number of records: no limit
Maximum key length: no limit
Maximum number of segments per key: 16
Maximum fixed record length: 65,535 bytes
Maximum variable record length: 2 GB
The basic guideline is to use isCOBOL ISAM Server if you require client/server, transaction management and/or an ODBC driver. Otherwise, use JISAM. Use JISAM especially if you require a pure Java solution (e.g. for accessing files on a mobile device).