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As I understand, the internal timer clock source on the STM32(F4) microcontrollers can be either APB1 or APB2. However, I can't find which timers get which clock.
I already found ST AN4013, which explains almost everything about the timers, but not their respective internal clock source.
Does anyone know, or have a source for, exactly which clock each timer uses?
The ST's Application Note you linked is just a generic description, not everything. The hardware detail is differ from each MCU models. ANs will only tell you overall idea. So you need to look at documents specifically written for each MCU model.
As the comments mentioned, when you work with peripherals of STM32 you will mostly need to look at two documents (as you didn't specified the MCU model I will give you example of STM32F407):
It is a brief description of the hardware. Since APB1 and APB2 are related with bus, the things you want is described in memory map section (aka. section 4 Memory Mapping)
It is very detailed (1749 pages!) description of the MCU. When you look at Timers in this manual you will realize there is a lot more stuff than the AN. Anyway this document also desribes memory map. (Section 2.3)
Note) Even though STM32 HAL API abstracts hardware detail you still need to know which APBs are connected to Timers you are using. For example, all peripherals shares common APB bus clocks. This means that if you change a clock setting of APB1, clocks of all peripherals connected to APB1, including Timers, will be changed as well. This might lead to unexpected timing changes of other unexpected Timers.
For example: MCU STM32F412 Document RM0090 "Memory and bus architecture" page 64 Table 1. STM32F4xx register boundary addresses
