With the recent announcement of the latest service pack release for the System Center 2012 Configuration Manager (ConfigMgr) product line (http://blogs.technet.com/b/configmgrteam/archive/2015/05/14/announcing-the-availability-of-sysctr-2012-r2-configmgr-sp1-and-sysctr-2012-configmgr-sp2.aspx) there seems to be a bit of confusion on what to install and in which order. There is some official documentation available at https://technet.microsoft.com/en-us/library/jj822981.aspx#BKMK_UpgradeVersions. I'm going to make an attempt to clarify it for everyone here as well.
|Starting version||Step1||Step2 (if needed)||Final version|
|Fresh||2012 SP2||2012 SP2|
|Fresh||2012 SP2||2012 R2 SP1||2012 R2 SP1|
|Fresh||2012 R2||2012 SP2||2012 R2 SP1|
|2012 SP1||2012 SP2||
|2012 SP1||2012 SP2||2012 R2 SP1||
2012 R2 SP1
|2012 R2||2012 SP2||
2012 R2 SP1
What may confuse people is that R2 SP1 is a very small file. It is essentially enabling the R2 feature set for those with the correct licensing to do so. An upgrade for R2 won't need it since that proper licensing will be detected from the current install.
Another note for those that have a hierarchy. Step1 will need to be done for the CAS and each primary site independently. Step 2 will only be necessary on the CAS and it will do the upgrade for the entire hierarchy.
On a related note, if you have a R2 SP1 DB backup and need to recover the site, running recovery from the SP2 media and pointing at the backup DB should work and give you back a fully functional R2 SP1 site.
5/29 update - Removed RTM upgrade path since 2012 RTM isn't supported.
6/1 update - Added 3rd "fresh" entry for clarification
9/15/15 - Point of clarification. "Fresh" means you have no ConfigMgr installed yet and you are wondering what DVD to put in the tray for your install.