There were so many different Archie Comics Sonic related Mini-Series!
Some of these may be harder to collect, so look carefully in order to complete your Sonic items collection. Anything that ran more than 1 issue with a somewhat continuous arc, regardless of whether it became ongoing, is shown here.
Time to go hardcore and complete your comic collection?
Then you can't miss these mini-series comics, even though Sonic is not in all of them. Out of these, the Princess Sally ones are probably the most difficult to get in original form. The Knuckles miniseries was so popular, that it led to him getting his own comic. 

This is the Sonic Quest mini-series. It featured a story vaguely along the lines of Sonic 3, wherein Robotnik tried to sink the Floating Island by using the Death Egg. Knuckles, Sonic and the Chaotix had to try and stop him.
The art consistency and story-arc were pretty good on this series. It wasn't anything to blow the fans away, but it was solid enough to sell well. It is not particularly rare to find, and is a good addition to the collection if you like Archie Sonic comics.