If you are the author of your software's license, you can choose whatever format you want. If you want to pick an existing license, study the text if there is a requirement to keep it in the original format as it was when you received it. The MIT license, for example, only says
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
I am not a lawyer, but to my understanding, that does not necessarily mean you have to include a copy of "the original text file" which contained the license (there is probably not even "the one canonic text file" for this license). And HTML is so widely used, and at its base still a "text format", that I think you can safely assume that people who are able to download, read or modify your source code know also how to read a file like "license.html".
However, if you publish an open source project, most authors typically want people to obey the license they choose. So it should be hard for others to overlook the license terms when you publish your code or its documentation. So I assume it will serve you most not to hide the text somewhere deep in an appendix at the last pages of your 300 pages user manual. Better put it in the top folder of your source tree, with a descriptive name "license.txt" or "license.html", so noone will have an excuse for not having found those terms.
