This is actually a tougher question to answer than I expected. I know that, overall, my favorite inversion is the vertical loop. However, there are a few other unique inversions that I find much more thrilling than typical loops, but I still prefer the loop in general. It might have quite a bit to do with the fact that the loop was the first inversion I experienced (and at a time when inversions other than standard loops and corkscrews didn't exist). And speaking of the first inversion I experienced, that inversion was Sooperdooperlooper's loop, which still remains one of my all-time favorites.
However, this is a loaded question that I feel I can't answer simply by citing the type of inversion that I prefer; instead I will point out some of the best (in my opinion)
specific inversions that I've had the pleasure of experiencing.
The great thing about loops is that they come in so many varieties. Let's start with my favorite...
There's
Schwarzkopf, as I've already mentioned, and his are generally the same size, with a few notable exceptions like on Olympia Looping, Magnum Force/Mindbender (Galaxyland), and of course Zonga (none of which I've actually ridden, unfortunately). Something about these loops rock my world. Sooperdooperlooper's is not as intense as most other Schwarzkopf loops due to the 57-foot, rampy first drop taken at only 45mph, but its almost circular shape makes it more intense than most other manufacturers' versions. The other Schwarzkopf loopers I've ridden are Scorpion, Mindbender (SFoG), Shockwave, and Laser, which feature more intense loops (especially Shockwave and Laser, where I usually grey out on the second of their back-to-back loops), and of course the shuttles King Kobra (KD) and Viper/Greezed Lightnin' (SFoG/SFKK, respectively, and currently the only coaster I've ridden in two different locations)--taking Schwarzkopf loops backwards kicks butt. Aside from their intensity, the trains' lapbar-only restraint design (again, with a few exceptions) allows for complete freedom of the upper body, which, in my opinion, is one of the major reasons Schwarzkopf loops are among the best.
Arrow loops are fun, too, but oddly they are all the exact same size no matter how large or small the coaster happens to be. For Arrow, it's all about how high the loop is placed. Take Cedar Point's Corkscrew, where the loop sits low to the ground; with an ~80' drop the loop is taken at the right speed. Then there's a coaster like GASM, where a loop of the same size is the first element after the massive 155' drop; obviously if it sat low to the ground like on Corkscrew, people would die.

So it's placed at the top of a huge incline, and the result is kind of a hyper-esque succession of huge drop and subsequent climb, but instead of the track levelling out to form an airtime hill, the track curves past vertical and sends you upside-down and in the opposite direction. And that first loop on GASM, even though it sits ridiculously high up, is mega-intense; you
slam into the top of that thing (hence, the
extra bracing on the top half). Some of the exceptional Arrow loopers I've ridden include Loch Ness Monster, Dragon Mountain, Anaconda, Canyon Blaster, GASM, and Vortex. Honerable mention goes to Python, formerly at SFA, formerly Adventure World...formerly Wild World.

While I prefer the simplicity of the Schwarzkopf shuttles, Arrow's was a twisted variation on Anton's that provided absolutely sick air before and after the loop (and it
should have also provided an oxygen machine at the top of the 47 flights of steps you had to climb to get to the loading platform).
However, all that aside, Arrow's crowning achievment is Tennessee Tornado's first loop, and in my opinion is one of the best inversions ever designed. This loop is a departure from the Arrow norm in that its entrance is close to the ground, yet is extremely tall like an average B&M loop. However, it doesn't have the typical exaggerated teardrop shape that B&M loops exhibit, and is therefore more circular in shape, more closely resembling Schwarzkopf or Togo loops. Because the entrance and exit are spaced
so far apart from each other, the track twists on the ascent and descent ever so slightly, but enough to notice when riding, which is a really cool feeling. That, coupled with the awesome hangtime at the top, is what sets this loop apart from the rest, and probably the primary reason I've placed Arrow loops just under Schwarzkopf's.
I've only experienced three, but
Togo loops are good in their own right. I know my opinion is unpopular, but I actually liked the Togo coasters I've ridden. Then again, judging from this thread, my affinity for vertical loops is in minority as well. Manhattan Express' loop is ok, but the ones that I really love are on the standups. King Cobra and Shockwave are my two favorite standups, and the loops contribute largely to that fact. I rarely ride these coasters anywhere but the front row because I love the feeling of freedom you get during the first drop and loop while standing up, with absolutely nothing in front of you. I get more of a flying sensation from the Togo standups than flying coasters. And the loops are shaped similarly to Schwarzkopf's (but larger), which is probably why I'm partial to them.
Finally, we have the
B&M loops, which are probably my least favorite overall. That is definitely not to say that there's anything wrong with them, however. B&M coasters I feel have a certain 'overengineered' feel to them (especially the later ones), and of course this applies to their loops as well. Similar to Togo, I actually prefer one type of coaster to another when it comes to B&M vertical loops, but it's not the standup. Rather, inverted loops in my opinion are generally better than the sitdown or standup loops I've been on. Alpengeist, my all time favorite invert, has a phenomenal loop, but it's easily on the same level as Talon's, Raptor's, Montu's, Great Bear's. I'd have to give the edge to both loops on Batman The Ride for their overall intensity, however, and ironically they're my least favorite of all the inverts I've ridden.
Last, but not least, I have to give credit to the single
Pinfari loop I've experienced, on Looping Star at Ocean City Pier Rides in Ocean City, MD. This loop can be described as a shrunken Schwarzkopf. I love the tight radius it has; really slams you with positive Gs.
Another honerable mention has to go to Son of Beast's loop, and I'm not so sure it's an outstanding loop on its own when compared to other loops. I'm
pretty sure it is, but sometimes I think it
seems so fantastic because it's a welcome 3 second break from the sheer hell of the rest of the ride.
So, I think I've covered vertical loops pretty thoroughly at this point. Like I mentioned at the top, though, there are a few specific inversions that I consider some of the best elements ever conceived. They are specific to only a select few coasters, some even one of a kind, which for me is a big plus, as I have a tendency to rank things higher just because of the unique factor. I'll run down the list of my favorite unique inversions--in no particular order--and why I like them:
Top Hat - Batman & Robin: The Chiller / Mr. Freeze (SFoT) - This is one of my all time favorites. It took me by surprise the first time, and I'm not sure I can even describe why it's so awesome. I think I like it because it reminds me of a loop, but with the entrance and exit track separated and straightened out. It really feels weird to me entering an inversion while heading upwards veritcally.
Twist & Dive - Viper (SFGAdv) / Manhattan Express - The twist & dive, in my opinion, is a bizarre variation of the B&M dive loop, but oh, so much better. Strangely, the two twist & dives I've experienced are actually quite different in the way they are executed. On Viper, after the first drop, the train banks hard to the left and climbs up to the next crest, the track twists to the right (the opposite direction of what is expected), and the train hangs upside down briefly before diving back to the left. The feeling is indescribable, and totally makes the coaster. On Manhattan Express, the twist & dive is entered immediately after the loop, and the entrance is a straight section of track that twists to the right, but there is more hang time than on Viper since the train is actually slowing down (the whole first half of the inversion is on an incline) until it curves downward and exits directly underneath the entrance track.
Wraparound Corkscrew - Drachen Fire - This inversion scared the bejeezus out of me the first time I rode Drachen Fire its opening year. Ok, it's basically just a corkscrew, but it was so high up...a bit unnerving back then. However, unlike a typical Arrow corkscrew, as you exit you don't find yourself right side up, but rather plummeting toward the Earth at breakneck speeds. One of the most killer 'first' drops on any coaster.
Cutback - Drachen Fire - Another one of a kind inversion, and on the same coaster. The cutback seemed to be the predecessor of the top hat, but not nearly as extreme. However, the element feels more closely related to a corkscrew than a top hat. The first half feels very familiar, as if you are heading into a typical corkscrew, but as you top out, the coaster suddenly 'chickens out' and heads back in same direction it came from. It doesn't sound all too exciting, but it's the unexpected result that really makes it work.
Flying Snake Dive - Storm Runner - Speaking of unexpected, this one takes the cake. I'm not sure if I'd be mentioning this inversion if it weren't for what leads up to it. To me, I feel like the whole sequence of airtime-hill-leading-into-heartline-roll-leading-into-snake-dive should be considered one complete element. Here's a quote from my 2004 trip report to Hershey regarding this element (or series of elements): "Climbing up the hill following the sidewinder, you can't even see what's coming. As you crest the top, massive ejector air ensues, and before you can even catch your breath, you're twisting into the barrel roll, which feels like it doesn't want to end. And it doesn't, until you're upside-down again, and then heading down and out before it feels like you should. It's the most convoluted element on a coaster yet."
Butterfly - Ninja (SFoG) - Vekoma's butterfly element can also be found on Goudurix, which has a reputation for being one of the roughest coasters around. Then again, Ninja doesn't have a stellar reputation either, but I really enjoyed it (must be that 'Togo gene' that only I and a few other enthsiasts I know have). The butterfly is comprised of the coaster's first two inversions, and from certain angles they almost look like two consecutie vertical loops, which isn't far from the truth. They are spaced somewhat far apart, so the connecting track from one to the other actually provides some nice laterals, and unexpected direction changes.
Well, that's about it. If you've read this far, I commend you for putting up with my long-winded babble. Oh, and one last thing--my least favorite inversion is probably the cobra roll. Not sure why, it just doesn't do much for me.