JavaCard is by far more popular, mostly because GSM SIM cards are based on JavaCard. At the same time, you need to pick Smart Card that better fits your specific project requirements, not by OS popularity. Here are some differences between MULTOS and JavaCard:

Quick Summary

• MULTOS is considered "more secure", and some government projects like ePassport have choosen MULTOS cards
• JavaCard is many times more popular in terms of numbers of cards in existence (billions), largely because GSM SIM cards are JavaCards
• JavaCards are usually much cheaper to acquire, and there are larger variety of vendors
• JavaCards allow using free open source tools to develop and load applications on card. Usually the only thing you need to pay for is Card Reader unit and Cards themselves
• Different Banks / EMV implementations use both MULTOS cards and JavaCards

Security Architecture

• native in MULTOS, for Javacard it is provided by GlobalPlatform
• uses asymmetric keys for MULTOS vs symmetric for Javacard / GlobalPlatform (??? is this true ???)
• uses a firewall to separate applications on card vs. off-card verification methods for Javacard
• applications / data loaded onto cards via secure packets for MULTOS vs a secure channel for Javacard / GlobalPlatform

Programming Languages

• Javacard - Java
• MULTOS - native assembly (MEL), C (most popular choice), and Java (mostly for porting code from JavaCard)

Interoperability Testing

• MULTOS has a mandatory approval process – provides confidence in the security and interoperability of MULTOS implementations.
• Testing is performed by independent 3rd party labs. This means that applications can be deployed on MULTOS platforms from multiple suppliers.

Generic Loading of Applications

• Once you have a script for loading applications to MULTOS, it does not need to be changed for each implementation or application.

Application Personalisation

• In MULTOS, Application personalization is usually done off-line in advance. In JavaCard, it is done at perso time on the perso machine.

Additional Background Information

• JavaCard was a natural progression from the growing use of the Java programming language in the 1990s while MULTOS was developed as an operating system for an electronic purse system and so the emphasis was always focused on high security to ensure fraudulent financial transactions could not occur. Also, JavaCard had received backing from Visa while MULTOS was endorsed by MasterCard.

References

• A much more detailed 30-page analysis of MULTOS vs JavaCard could be found here: http://jkremer.com/White%20Papers/MULTOS%20and%20JAVACARD%20White%20Paper%20JKCS.pdf

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