Here are a few I can think of, not all are necessarily things that I miss, but people do miss it.
- Gmail old style compose/reply dialog
- Windows 7 had a search everything feature, now windows 8 has search by App/Files/Settings
- Github used to have a downloads tab for you to upload binaries associated with your code.
- Internet Explorer 9 supported extensions (via plugins), IE 10 is plugin free (although a step forward) doesn't have any customizability (no potential ad-block / vimium)
- Twitter List functionality (it wasn't implemented well but it was useful to help separate your stream).
- OneNote- Older versions of OneNote had OCR functionality, newer ones don't, one of the reasons I prefer Evernote