What programming languages where used to write programs for Workbench 3.1

[Kronos]

Well, you are talking 68k so the options are (allmost) endless:

Various C compilers: StormC, GCC, Maxon(HiSoft)C, Manx, Lattice(SAS),Dice
A horde of assemblers : AsmOne,AsmPro,DevPac,OMA,PhxAss ......
The Wirth-trio : Pascal (HiSoft/Maxon) Modula2, Oberon
The just weird : Amiga-E
Obscure Basic-dialects: AMOS, BlitzBasic, ACE

Sure I've missed atleast half of them.

[Kronos]

The apps you list all come from the OS2.0 - 3.x period, so they are most likely useing a combination of gadtools and boopsi. See the Amiga-DEV-CDs for imformation and examples for that. Some might use obscure GUI-toolkits like StormWizard or Triton, you don't really want to go anywhere near these.

if you want to start with developing GUI-driven Amiga-SW today I'd recommend starting to learn MUI (SDK can be found on Aminet).