About 2 months ago I just upgraded us from SP3 to SP6. I did run into an issue with our SSO login. Received errors after logging in. Had to work with HP to resolve the issue. If you do not use SSO to login then level of effort is not much take about 30 min to install the SP. If you are using SSO then you may need HP's help on it. In the 2 months we have found no issues running SP6.
As far as I am aware: the biggest concern is JDK upgrade which is applicable upwards of 7.5 Sp5. So if you had any security settings in JDK 1.5 you need to reapply/migrate them in JDK 1.6. regards, Koya
As soon as you logged in you will see an error. This does not seem to happen with all users that are running SSO and PPM as I was talking to another company running PPM with SSO and they did not have an issue. If you have tested this and do not see the issue then you will be fine.
I have installed SP6 at another instance, running without siteminder and may most serious issue was related to the cookies, because at this SP was changed the XSS validations, then my issue was with the SAP and PPM interaction, if use SAP and after PPM we were unable to login to PPM, but it was a misconfiguration at SAP side.