If it weren't for the server running ADCS then I wouldn't be as worried; however here is what I would do:
1) Make sure you have a good backup of the 2008 DC; take one right before the upgrade.
2) Make sure that no FMSOs are owned by the 2008 DC; if there are any that it holds, transfer them to other DCs and give your environment time (or force replication through Sites and Services) to replicate changes to other DCs.
3) Make sure that you have at least one other GC domain controller in your environment; if you don't, go make another DC a Global Catalog.
4) Call Microsoft about the AD Certificate Services as I'm unsure of any potential pitfalls related to it when upgrading to a higher version of the same OS.
Typically there are feature sets that are added, but in the case of 2008 R2 Standard vs. Enterprise I usually see people pick Enterprise for the licensing bonuses and not feature set bonuses. Enterprise versions of 2008 R2 give admins the right to run the host + 4 VMs whereas Standard is only the host + 2 VMs in Hyper-V and other virtualization platforms. You also get unlimited RRAS and IAS network access connections for Enterprise vs the Standard with a limited amount. These are just a few examples of the many.
That being said, my 5th and final step would be to do the upgrade. Simply run through it like you would any other install/upgrade of Windows and make sure to choose upgrade rather than custom install (hopefully common sense here) on the installation screen, and also make sure to select the 2008 R2 install as the one you're upgrading. There usually aren't any issues when doing an in-place upgrade like this, but that's why you have backups; plus I've not done an in-place on a server running ADCS.