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Apologies for some duplication of existing threads related to this. It appears as if the answer to this is here:
Re: Upgrade Patches for 10g AS(10.1.2)
I also found this in Oracle Doc ID: 329361.1:
Security Alerts / Critical Patch Updates+
Oracle currently delivers the latest Critical Patch Updates on a quarterly basis: January, April, July, and October of each year. You should continually install these updates to secure your installation. Look for the latest update, and an associated Oracle Application Server Pre-Install Note, which will contain the latest patches to apply to your Oracle Application Server 10.1.2.x homes:
Critical Patch Updates (CPU) and Security Alerts Check for latest CPU, then look for an associated Patch Availability Note
Other Important Updates:
+[These are not entirely covered by above Patchsets or CPU]+
Note 417277.1 2007 Daylight Saving Time Updates For Oracle Application Server
Note 360870.1 Impact of Java Security Vulnerabilities on Oracle Products
Note 272808.1 How to Update the default JDK Installed in Oracle Application Server 9.0.4 and 10.1.2
Aside from the three exceptions above, I'm going to assume that all I need to do is apply the July2009CPU as it is cumulative and includes all previous updates provided since patchset 3. If anyone has anything to add/clarify please do.
CPU tells you what patches to install, so, after install them usually using opatch utility, you have to uset opatch -lsinventory (or something like it) and it has to show you all the patches insalled, it has to be in the list the one you just had installed.