Great to hear that you've got this well thought out. I'll answer the questions you had in the order I originally had, to keep the tempo.

1. Example API Call:

// Use this syntax in a button, it will add the URL to the page's script includes
{!REQUIRESCRIPT('/soap/ajax/20.0/connection.js')}

function doUpdate() {
  var updatedRecords = "get data from SwivelScript here as an array of named index arrays (or just arrays)"
  var records = new Array()
  for(var record in updatedRecords) {
    var newRecord = new sforce.SObject("Account") // Type of record here
    newRecord["Id"] = updatedRecords[record].Id
    newRecord["Name"] = updatedRecords[record].Name
    newRecord["Custom_Field__c"] = updatedRecords[record].Custom_Field__c // You get the idea
    records.push(newRecord)
  }

  // use async callback method
  sforce.connection.update(records, { onSuccess : processResults, onFailure : displayError } )
}

function processResults(results) {
  // everything went well with API, check results
}

function displayError(errors) {
  // something bad happened, bad field name, etc
}

// Do your code here, then call doUpdate()

doUpdate()

2. To clarify, programs like Microsoft Word will paste different data depending on the target application. As a simple example, open an HTML editor, Microsoft Word, and Notepad. Type some words into Word, apply some formatting, then copy and paste both into your HTML editor and Notepad. In Notepad, you'll see only the text without formatting (obviously, because Notepad does not support formatting). Your HTML editor should retain the formatting you placed in Word when you paste from Word. As long as your script can identify itself as a Rich Text capable input to the OS, you should be okay. I believe your statement that you have "raw access" to the clipboard suggests that formatting should be preserved when possible.

3. I won't lose too much sleep over it, because most likely it's more of a pipe dream; bookmarklets are extremely simple scripts that are browser dependent. However, I do think that some developers might make some chrome extensions for Firefox to support SwivelScript integration...

4. You don't necessarily need to determine the precise application, I just think it'd be nice if the clipboard data was in several formats and the recipient application can choose the most appropriate format. Windows (and I believe the other OS's) supports placing multiple objects in the clipboard with each object representing a different format of the same data. Giving a line-based format and a CSV-based format might be sufficient for most uses, along with a Rich Text format for fields that support it.

5. I'm glad to hear about the IM bit. Again, if you can grab the data in a Rich Text format when applicable, it would go a long way in improving readability when it gets to Salesforce.

6. I'd say hammer out the GUI logic first, then worry about esoteric cases such as connecting to ODBC. I would anticipate that 90% of users would want to do some fancy editing and/or moving data into and out of their normal applications, while connecting to a database that runs as a service or daemon is probably something that only consultants and developers would really care about (and occasionally the System Administrator that actually learned how to move beyond reporting and customization). I'd be willing to wait for this for v2 as long as v1 was a rock solid performer.

7. If you can cover Red Hat, Fedora, and Debian, with Gnome and KDE, you'll have nearly 100%  the Linux GUI covered, since command-line users wouldn't be able to use this script anyways. I would say RH would be the primary focus, since they position themselves as an "Enterprise Linux" and are probably the most common Linux in production environments (if I'm wrong, please let me know!).

Like I said before, great stuff, and I hope it works out well. If you need someone to toy around with it, let me know!