I have several of these that I like to follow... although not all of them are what I'd call "small"
St. Etienne - French Ligue 1... even though it's larger, and very popular in France, I love the support they have for the club, and I didn't even become a fan of the club until they were actually in the 2nd division... so now seeing them get success at the top level again is cool to see.
Celtic FC - Yeah, they aren't small at all whatsoever (if they were in the EPL they'd be one of the most massive clubs due to their ridiculous support - and along with Rangers would probably make the whole of the League far more interesting - not that I'm a fan of the idea...) Mostly because my nanny growing up was a staunch Celtic supporter from Glasgow and she's the one who got me into the sport in the first place from a young age... I had to deal with that whole 1990's terribleness of the club too for a while... thank god for Henrik Larsson... They also made the Champions League quite frequently whereas Newcastle does not so much especially these days - and were the opposing team to Newcastle in Alan Shearer's testimonial, and that was AWESOME.
And as for my REALLY small club that I follow, it's gotta be NAC Breda from the Eredivisie in Holland... They're definitely entertaining to follow.. however they're one of those clubs who are ever indebted and therefore dont do much in the league... But seeing them succeed brings a bit of a smile to my face....