Spoof - Redirect traffic using ARP Spoofing, DNS Spoofing or ICMP Redirects
BeEFAutorun - Autoruns BeEF modules based on clients OS or browser type
AppCachePoison - Perform app cache poison attacks
BrowserProfiler - Attempts to enumerate all browser plugins of connected clients
CacheKill - Kills page caching by modifying headers
FilePwn - Backdoor executables being sent over http using bdfactory
Inject - Inject arbitrary content into HTML content
JavaPwn - Performs drive-by attacks on clients with out-of-date java browser plugins
jskeylogger - Injects a javascript keylogger into clients webpages
Replace - Replace arbitary content in HTML content
SMBAuth - Evoke SMB challenge-response auth attempts
Upsidedownternet - Flips images 180 degrees

So far the most significant changes have been:

Spoof plugin now supports ICMP, ARP and DNS spoofing (DNS Spoofing code was stolen from https://github.com/DanMcInerney/dnsspoof/)
Usage of third party tools has been completely removed (e.g. ettercap)
Addition of the BrowserProfiler plugin
Addition of the JsKeylogger plugin
Addition of the BeefAutorun plugin
FilePwn plugin re-written to backdoor executables and zip files on the fly by using the-backdoor-factory https://github.com/secretsquirrel/the-backdoor-factory and code from BDFProxy https://github.com/secretsquirrel/BDFProxy
Added msfrpc.py for interfacing with Metasploits rpc server
Added beefapi.py for interfacing with BeEF's RESTfulAPI
Added Replace plugin
Addition of the app-cache poisoning attack by Krzysztof Kotowicz
JavaPwn plugin auto-detects and exploits clients with out-of-date java plugins using the Metasploit Frameworks rpc interface!!