- Is there a standard protocol for each of these frequencies?
With many of these frequencies there is (international) standards that define communication characteristics and protocols. Note, however, that this does not necessarily mean that there is exactly one protocol per frequency. If you take, for instance, 13.56 MHz, there is ISO 14443 (which itself defines two completely different low-level communication protocols), ISO 15693 (also containing multiple modulation and coding schemes), FeliCa, ISO 18092 (NFC), a number of protocols defined in ISO 18000, and possibly more. Besides the standardized protocols there are also several manufacturer-specific/proprietary RFID protocols. So just using the same frequency does not indicate compatibility.
- Is it possible to read any {insert frequency} RFID card/tag with any {insert frequency} RFID reader/encoder?
No, not at all. However, both, reader and card/tag manufacturer will typically state to what standards their product complies, so you can match the supported standards (or proprietary protocols). Moreover, many RFID readers typically support multiple standards/protocols within one frequency range (some readers support even multiple frequency ranges).
- Is there a difference between cards/tags in different shapes?
Shape and supported protocols/standards are usually independent of each other (with the exception of antenna shape which correlates with the supported frequency). So if they comply to the same standards/protocols, then they can be used interchangeably. But keep in mind, that this also means that one shape does not necessarily indicate a specific frequency/protocol/standard. E.g. there exist such keyfob type tags for at least different standards at 13.56 MHz and at ~125 kHz.
- Are all cards re-writable or are there also read-only ones?
Both types of cards/tags exist for most standards/protocols. Particularly in the ISO 14443 area, there also exist cards/tags with processing capabilities (i.e. cards that contain and execute (customizable) software instead of being pure memory).