Just for the fun of it, I dove in and manually minified the code further, without changing any semantics at all. With the following, I got it down from 2878 bytes to 2010 bytes which is a 30% saving:

!function(e,t){"object"==typeof exports&&"undefined"!=typeof module?t(exports):"function"==typeof define&&define.amd?define(["exports"],t):t(e.pell={})}(this,function(e){"use strict";var t,n=Object,i=document,o=prompt,r="pell-",a="button",u="className",l="appendChild",d="createElement",c="insert",s="rderedList",f="Horizontal",p="formatBlock",m="Enter the ",b=n.assign||function(e,i,o,r){for(i=arguments,t=1;t<i.length;t++)for(r in o=i[t])n.prototype.hasOwnProperty.call(o,r)&&(e[r]=o[r]);return e},g=function(e,t,n){return{icon:e,title:t,result:n}},h=function(e,t){return i.execCommand.bind(i,e,!1,t)},k=function(e){return/^https?:\/\//.test(e)?e:"http://"+e},L={bold:g("<b>B</b>","Bold",h("bold")),italic:g("<i>I</i>","Italic",h("italic")),underline:g("<u>U</u>","Underline",h("underline")),strikethrough:g("
S
","Strike-through",h("strikeThrough")),heading1:g("<b>H<sub>1</sub></b>","Heading 1",h(p,"<H1>")),heading2:g("<b>H<sub>2</sub></b>","Heading 2",h(p,"<H2>")),paragraph:g("¶","Paragraph",h(p,"<P>")),quote:g("“ ”","Quote",h(p,"<BLOCKQUOTE>")),olist:g("#","Ordered List",h(c+"O"+s)),ulist:g("•","Unordered List",h(c+"Uno"+s)),code:g("&lt;/&gt;","Code",h(p,"<PRE>")),line:g("―",f+" Line",h(c+f+"Rule","<PRE>")),link:g("","Link",function(){(t=o(m+"link URL"))&&h("createLink",k(t))}),image:g("","Image",function(){(t=o(m+"image URL"))&&h(c+"Image",k(t))}),undo:g("↺","Undo",h("undo")),redo:g("↻","Redo",h("redo"))};e["default"]={init:e.init=function(e){var o=e.classes,c=e.actions,s=i.getElementById(e.root),f=i[d]("div"),p=i[d]("div");p.contentEditable=!0,f[u]=o.actionbar||r+"actionbar",p[u]=o.editor||r+"editor",p.oninput=function(t){return e.onChange&&e.onChange(t.target.innerHTML)},s[l](f),s[l](p),(c?c.map(function(e){return"string"==typeof e?L[e]:b({},L[e.name],e)}):n.keys(L).map(function(e){return L[e]})).forEach(function(e){t=i[d](a),t[u]=o.button||r+a,t.innerHTML=e.icon,t.title=e.title,t.onclick=e.result,f[l](t)})}},n.defineProperty(e,"__esModule",{value:!0})})

However, when you consider gzipping, this represents savings of roughly 12–16 bytes (it depends a little on whether the files are noeol and whether you avoid file metadata going in the gzip stream—pro tip, make your gzipped files smaller with `gzip < x > x.gz` instead of `gzip x`). Quite a few of the latter “save another one or two bytes” tricks that I employed not only increase runtime trivially (e.g. concatenating two string literals instead of using one string literal), but they also increased gzip size by four or more bytes. (The tricks for the strings “Enter the ”, “Horizontal”, “rderedList” and “insert” had saved seven bytes ungzipped at the cost of about 21 bytes gzipped, and “pell-” and “button” had saved one byte at the cost of eleven gzipped.) The lesson there is—gzip is pretty good, and deduplication is normally a waste of time in tiny files! I was hoping to get it under 2048 bytes raw and 1024 bytes gzipped; I achieved 2048 bytes raw, but after undoing some of the silly tricks gzipped is still 60 bytes off.

Of course, if you decide to abandon AMD/CommonJS support, you can quickly whip 210 bytes (100 gzipped) off, but that’s a change in semantics so I can’t count that despite it getting it under 1000 bytes.