I do a fair amount of diving in SE Florida. I'm not sure how 'off the beaten path' any of these are but the places I've dove and really enjoy are:
Jupiter is the best (I usually make 50+ dives per year in Jupiter, mostly with Jupiter Dive Center). If you like big marine life encounters (sharks, turtles, goliath grouper, big moray eels) this is the place for you. Some of the ledges are very dramatic. Tunnels is a good site for shark encounters and the Bonaire wreck trek for goliath grouper.
West Palm Beach is also very nice. Slightly prettier reefs and some sites have just as much big marine life as Jupiter. West Palm Beach also has the Blue Heron Bridge beach dive site (see the Blue Heron Bridge Toll thread for info). I like the Mispah wreck trek the best of the boat diving sites, but almost all the reefs are nice too.
Boynton Beach has some very beautiful reefs and at least one wreck (Castor) known for its Goliath Grouper population.
Pompano: I just dove with South Florida Dive HQ last weekend and had a fantastic time on the 60 foot reef line. The tropical fish life was incredible: we also got lucky and saw 4 dolphin while diving. There is also a reef line that is 25 feet deep that can be beach dove (long swim) or from a boat. Most of the local operators go to the shallow and deeper sites. Pompano also has some very nice wrecks. Look on South Florida Dive HQ's or Scubatyme's websites for a listing of all the wrecks.
Lauderdale by the Sea: the beach diving is incredible: just a short swim. Gold Coast Scuba has a club and rents gear. Force E is another good shop. There are some quaint resturants in the area too (near the pier).
Dania Beach: also a very nice beach dive that in some ways is superior to LBTS because the reef has a bit more relief than LBTS but is a longer swim.
Key Largo/Islamorada: lots of pretty reefs and the four major deep wrecks. One of the nice deep reefs is Conch Wall: not many operators seem to go there on a regular basis, but I know Conch Republic has it scheduled periodically.
Key West: the Vandenberg.
Probably more off the beaten path: consider a 3 day live-aboard to the Dry Tortugas. I've taken trips on the MV Spree and Ultimate Getaway. Both are similar and very fine boats. The MV Spree doesn't do spearfishing trips while a majority of Ultimate Getaway's trips are spearo trips.