I would like all my toolkit to use UTF-8 but find that some tools on Windows seem to use CP1252 (which appears to be Windows-specific). Does this create output which is incompatible and if so at which codepoints? If so, can I do anything about it?
(I don't completely understand the issues so I'd be grateful for basic education on these encodings).
Tools hard-coding for code page 1252 on Windows is very unlikely. Much more likely is that it happens to be the default code page on your machine. 1252 is used in Western Europe and the Americas. It is configured in Control Panel, Regional and Language options. They've been using different names for it, on Win7 it is in the Administrative tab, Change System Locale.
Yes, many tools use the default code page unless they have a good reason to chose another encoding. The BOM is such a good reason. Notable examples are Notepad (unless you change the Encoding in the File + Open dialog to something else than Ansi) and C/C++ compilers. There typically isn't anything special you need to do to use the default code page. Guessing the correct code page for a text file when you don't have a BOM is impossible to do accurately. Google "bush hid the facts" for a very amusing war story.