In most cases, your fonts will work in applications no matter what glyph names are used. However, for OpenType PS (.otf) fonts, glyph names do play a role when fonts are embedded in PDF files and the user tries to search or copy-paste the text. In such cases, Acrobat uses glyph names as a help to determine what text actually is saved in the PDF.
At http://partners.adobe.com/asn/tech/type/unicodegn.jsp , Adobe publishes their recommendations for glyph naming. These recommendation were revised a few times. Initially, Adobe recommended names such as "Asmall" for small caps, and used them in their older OpenType fonts. More recently, the recommendation changed to "A.sc", and this the naming currently used in Adobe fonts. For Acrobat to perform text searches, only the glyph name portion before the period are important. This way, "A.sc" would be mapped to the letter "A", while "Asmall" is mapped to nothing (or a Unicode from the Private Use Area which has no meaning).
My recommendation is that, whenever possible, glyph name extensions (after the period) whould correspond to the OpenType Layout features they're used in. The small caps feature is identified as "smcp", so using names such as "A.smcp" would be permittable, although in this special case, I'd also accept "A.sc". For other features, I strongly recommend using the OpenType Layout features codes. For example, since old-style numerals are abbreviated "onum", the glyphs should be named "one.onum", "two.onum" etc.
But again, the glyph name extensions are purely a convention.