A module for Reddit Enhancement Suite (RES) which finds any subreddit mentions that are not links and converts them into links.

RES Module - Subreddit Linker.js

modules['subredditLinker'] = {
    moduleID: 'subredditLinker',
    moduleName: 'Subreddit Linker',
    options: { },
    description: 'Finds any subreddit mentions that are not links and converts them into links.',
    isEnabled: function() {
        return RESConsole.getModulePrefs(this.moduleID);
    },
    include: Array(
        /https?:\/\/([a-z]+).reddit.com\/user\/[-\w\.]+/i,
        /https?:\/\/([a-z]+).reddit.com\/[-\w\.\/]+\/comments\/[-\w\.]+/i,
        /https?:\/\/([a-z]+).reddit.com\/message\/[-\w\.\_\?=]*/i
    ),
    exclude: Array(
        /https?:\/\/([a-z]+).reddit.com\/ads\/[-\w\.\_\?=]*/i,
        /https?:\/\/([a-z]+).reddit.com\/[-\w\.\/]*\/submit\/?$/i
    ),
    isMatchURL: function() {
        return RESUtils.isMatchURL(this.moduleID);
    },
    go: function() {
        if ((this.isEnabled()) && (this.isMatchURL())) {
            // DOMNodeInserted listener and findAllLinks code are based on / shamelessly copied from Show Images module.

            document.body.addEventListener('DOMNodeInserted', function(event) {
                if (
                    ((event.target.tagName == 'DIV') && (event.target.getAttribute('id') == 'siteTable')) ||
                    ((event.target.tagName == 'FORM') && (event.target.getAttribute('class') == 'usertext'))
                )
                {
                    var isSelfText = false;
                    if (event.target.tagName == 'FORM') {
                        isSelfText = true;
                    }
                    modules['subredditLinker'].findAllLinks(event.target, isSelfText);
                    if (!isSelfText) {
                        modules['subredditLinker'].waitForScan = setInterval(function() {
                            if (!(modules['subredditLinker'].scanningForLinks)) {
                                modules['subredditLinker'].subredditLinker(modules['subredditLinker'].gw, true);
                                clearInterval(modules['subredditLinker'].waitForScan);
                            }
                        }, 100);
                    }
                }
            }, true);
            
            this.findAllLinks();
        }
    },
    checkElementForLinks: function(index) {
        ele = this.allElements[index];
        var children = ele.childNodes;
        for (var i = 0; i < children.length; i++) {
            if (children[i].nodeType == 3) {
                // Only search in Text Nodes to avoid modifying items that are already links.

                var text = children[i].nodeValue;
                var searchStart = 0;
                var tag = children[i].parentNode.tagName;
                var linkPattern = /(^|\b|\s)(https?:\/\/)*([a-z]*\.)*(reddit\.com\/)*\/?r\/([a-z0-9_]+)/gi;
                var matches = text.substring(searchStart).match(linkPattern);

                if (matches != null) {
                    for (var j=0; j < matches.length; j++) {

                        // Break content into 3 parts based on location of the match.
                        var match = matches[j];
                        var matchIndex = text.indexOf(match,searchStart);
                        var before = text.substring(0,matchIndex);
                        var after = text.substring(matchIndex + match.length);

                        //console.log('Match:' + match);

                        // If http(s) and/or the (sub)domain were included, preserve that info, otherwise build from scratch.
                        var subUrl;
                        if ( match.search(/^https?:\/\//i) > -1 ) {
                            subUrl = match;
                        } else if ( match.search(/^([a-z]*\.)*reddit.com/i) > -1 ) {
                            subUrl = "http://" + match;
                        } else {
                            var subName = match.substring(match.indexOf("r/"));
                            subUrl = "http://www.reddit.com/" + subName;
                        }

                        // Create link.
                        var subLink = "<a href=\"" + subUrl + "\">" + match + "</a>";
                        searchStart = matchIndex + subLink.length;
                        text = before + subLink + after;
                    }
                    var newNode = document.createElement(tag);
                    newNode.innerHTML = text;
                    children[i].parentNode.replaceChild(newNode, children[i]);
                }
            }
        }
    },
    findAllLinks: function(ele, isSelfText) {
        this.scanningForLinks = true;
        if (ele == null) {
            ele = document.body;
        }
        // get elements common across all pages first...
        // if we're on a comments page, get those elements too...
        var commentsre = new RegExp(/comments\/[-\w\.\/]/i);
        var userre = new RegExp(/user\/[-\w\.\/]/i);
        this.scanningSelfText = false;
        if ((commentsre.test(location.href)) || (userre.test(location.href))) {
            this.allElements = ele.querySelectorAll('.expando .usertext-body > div.md p, .expando .usertext-body > div.md li, .expando .usertext-body > div.md em, .expando .usertext-body > div.md strong, .content .usertext-body > div.md p, .content .usertext-body > div.md li, .content .usertext-body > div.md em, .content .usertext-body > div.md strong');
        } else if (isSelfText) {
            // We're scanning newly opened (from an expando) selftext...
            this.allElements = ele.querySelectorAll('.usertext-body > div.md p, .usertext-body > div.md li, .usertext-body > div.md em, .usertext-body > div.md strong');
            this.scanningSelfText = true;
        }
        if (this.allElements != null) {
            // Make sure it doesn't die if there are no elements to work with, which happens in the message window if there are no messages.
            this.allElementsCount=this.allElements.length;
            this.allElementsi = 0;
            if (RESUtils.pageType() == 'comments') {
                (function(){
                    // we're on a comments page which is more intense, so just scan 15 comments at a time...
                    var chunkLength = Math.min((modules['subredditLinker'].allElementsCount - modules['subredditLinker'].allElementsi), 15);
                    for (var i=0;i<chunkLength;i++) {
                        modules['subredditLinker'].checkElementForLinks(modules['subredditLinker'].allElementsi);
                        modules['subredditLinker'].allElementsi++;
                    }
                    if (modules['subredditLinker'].allElementsi < modules['subredditLinker'].allElementsCount) {
                        setTimeout(arguments.callee, 1000);
                    } else {
                        modules['subredditLinker'].scanningSelfText = false;
                        modules['subredditLinker'].scanningForLinks = false;
                    }
                })();        
            } else {
                var chunkLength = modules['subredditLinker'].allElementsCount;
                for (var i=0;i<chunkLength;i++) {
                    modules['subredditLinker'].checkElementForLinks(modules['subredditLinker'].allElementsi);
                    modules['subredditLinker'].allElementsi++;
                }
                modules['subredditLinker'].scanningSelfText = false;
                modules['subredditLinker'].scanningForLinks = false;
            }
        }
    }
}

Forked to remove trailing semicolon.