Microsoft just released Update Rollup 3 for Dynamics CRM 2013 (download here also listed in my resources page) and I want to clarify the current situation regarding update rollups and service packs.
With the release of the Service Pack 1 Microsoft incremented the product number version, from 6.00 to 6.01, but with the Update Rollup 3 (related to the 6.00 version) they make official the division in two routines, one with the SP1 installed, one without the SP1.
The current paths are:
1) CRM 2013 RTM (6.00) → UR1 (6.00) → UR2 (6.00) → UR3 (6.00) → ... (6.00)
2) CRM 2013 RTM (6.00) → UR1 (6.00) → UR2 (6.00) → SP1 (6.01) → ... (6.01)
The confirmation is inside the KB for the Update Rollup 3:
If Update Rollup 3 is applied, we recommend that you wait until Update Rollup 1 for Microsoft Dynamics CRM 2013 Service Pack 1 (SP1) is available before you upgrade to the Service Pack 1 release stream. This is because Update Rollup 3 may contain fixes that are not included in Microsoft Dynamics CRM 2013 SP1.
Bottom line: if you already installed SP1 in your environment, you need to wait for the release of the specific Update Rollup for SP1.