Sourcing parts with standard geometry
Many major electronics suppliers (Mouser, Digikey) have parametric searches, so you can specify, for example, what transistor package you're looking for, or what potentiometer shaft diameter or mounting type you want. If you're looking for the most flexibility (swapping/upgrading/adjusting parts as needed) I'd suggest the following;


Choosing a specific transistor package and pinout, or designing your PCB for easily accommodating variations.
The power jack depends on what you need to supply, really. If you need DC then there are numerous designs, I typically use a 2.1mm jack like this. But by all means, let us know what your specific needs are.
Virtually all potentiometers I use have 1/4" shafts, requiring a 3/8" mounting hole. The case size is often labeled (somewhat confusingly) 16mm. 24mm is also common.
As for fans, I suggest choosing a specific voltage (5V and 12V are common) and size (there are a few standard computer sizes). There are a few different types of connectors, so what you could do is cut them off and use spring or screw terminals on the PCB to connect them to your circuit.


Of course, I'm making a few assumptions (you'll be mounting things on some sort of chassis or panel, and by potentiometer you don't mean a trimmer) but again, feel free to specify your needs/intentions and we'll be happy to clarify. I realize I haven't exactly specified standards per se, but my aim was to show you some regularly available options.