The official development tool is the Microsoft 6809 Assembler cartridge.
A patched and improved version of it is available. For older machines it needs to be put on a ROM in a real cartridge, but for the TO8/D/9+ it can also be used as a CHG resident program.
An alternative is AssDesass, which runs as regular software loaded from tape or disk.
On MO5/6, there is also ODIN
Graphics
Colorpaint
Graffiti
Pictor
Music
Music 3V (3-channel music for MO6/TO8)
Cross development tools
Emulators
TEO - Emulator for TO machines, fairly accurate, with built-in debugger. Linux and Windows, open source.
JTEO (Java port of the above)
MESS - Rather accurate emulation for all machines, built-in debugger, multi platform, open source.
dcmoto - Emulator for all Thomson machines, Windows only, closed source. Usually runs existing software well, but may behave unexpectedly with new code.
dcmo5, dcto8d, dcmo6 - Older version of the above,. One emulator per machine. DCMO5 and DCTO8D are open source and multiplatform, but DCMO6 is not.
marcel'o'5 - Older emulator, not very accurate. Open source.
Assemblers
lwtools modern cross macro assembler with lots of features.
c6809
C compilers
gcc6809 modern compiler using lwtools for assembling and linking.
mc09, K&R compiler, smaller but more limited.
Graphics
GrafX2, the ultimate 256-color painting program, features a color constraint checker for Thomson
png2mo5 converts PNG files to the Thomson screen format. It works for TO machines, too.
SDK/Toolkits
cc90
PulkoMandy's Thomson stuff Source for various demos and other software, and several small tools for managing floppy and tape images, and so on. Open source, very portable code.