I think a better way to think of this may be in terms of canonicalization. Inside your application, you should decide on a single canonical way to represent data, one which fits the type of processing and expected use of the application. For example, you might decide that all strings should be UTF8, and should be interpreted (and stored) as whatever the user initially wrote. You might decide that any structured data should be parsed and then stored as protobufs in a BigTable. Or you might decide that an RDBMS is your native datastore and use whatever the native string encoding is for it, as well as parse & normalize data into tables upon input.

Then, whenever you take input, your job is to validate and encode it. If you get a Windows-1252 string, you should re-encode it to utf8 for further storage. If it has data that are invalid UTF-8 codepoints, you should either strip, replace with a replacement character, or notify the user with a validation failure. Same with structured data that fails your normalization rules - you should usually notify the user.

And when you send output, you should escape based on the intended output device. If you're putting it in an HTML page, HTML-escape it. If it's a URL, url-encode it. If it's a database query, SQL escape it. If it's a CSV, quote it.

Thinking in these terms keeps the internal logic of your application simple (there are no format conversions except at system boundaries), and it also gives you a lot of flexibility to preserve the user's intent and add new output formats later.