Do you mean actual reigns, or wrestlers' qualities? I'm gonna talk about reigns. Btw, I don't really like all this "World Champion" gaga/gimmick, I prefer the term "major champion".
Anyway, Top 5:
1. Johnny Gargano
(Open the Freedom Gate Champion of DGUSA)
Great reign as the DGUSA Champion, he's won it in November 2011 and has defended it succesfully 5 times. His first defense against Ricochet (Evolve 10) makes his reign epic alone, after all the shit he had to fight through in that match. The Yoshino V2 defense from Miami was excellent, and so was the Fox V3 defense. The Taylor defense was good enough, and the latest Tozawa V5 defense was bloody awesome. Johnny Gargano made aleready the title even more relevant.
2. Eddie Kingston
(Grand Champion of CHIKARA)
An awesome reign by CHIKARA's Kobashi, he's the top dog who holds the major title, very simple and effective booking. This lineage speaks for itself:http://www.chikarapro.com
The Jigsaw defense was bloody great, and I can't wait to see the Sara Del Rey defense./titlesGRAND.shtml
3. CM Punk
Somehow irrelevant until the recent heel turn, but the matches produced by this reign were usually good/great. Ziggler, Henry, Bryan, Jericho, a ton of ***+ defenses. Sure, Punk's character fucking sucks, but you can't deny the in-ring work in his reign.
4. Jun Akiyama
(Triple Crown Champion of All Japan)
This bald motherfucker won the title on October 23rd in the epic clash against Suwama, and has successfuly defended it 4 times (Kea x2, Omori, Mutoh). His next defense si against legendary Pancrase founder Masakatsu Funaki, somewhere in August.
(Open the Dream Gate Champion of Dragon Gate)
Dragon Gate's icon has a pretty good and believable reign. I didn't see his latest Tozawa defense, but the two awesome bouts against Jimmy Susumu and PAC make this reign Top 5 worthy alone.