I think the companion I've seen the least running around is Skadge.
On my merc I mostly use Mako and Blizz. Mako, just because my bh was my first main character and I was too used to her by the time I picked up the next companion, and Blizz cause he's adorable. Skadge stays on the ship, always, don't even send him on crew missions (the -1000 pts he's carrying would make him fairly useless there anyway). If I could find a way to airlock him, I would, but he will never smell planet air.
My vanguard uses Jorgan almost exclusively (heavy armor dps + heavy armor dps = crap just DIES). Once in awhile I'll pull out the others just to put them through their paces, but 99% of the time I run with Jorgan. M1-4X probably gets used the least just because of gear.
My sentinel uses Scourge and Kira, mostly Scourge. I like Scourge
Rusk gets used the least cause he's ridiculously irritating. T7 has better gear than any of my other droid comps since I had him geared for the last fight, but if I'm using a tank, I'm using Scourge.
My sage uses Zenith almost always. On rare occasions I'll pull out Iresso, but it usually only lasts a fight or two and then Zenith comes back out. Nadia gets used the least cause her voice grates on my nerves.
My operative uses Vector mostly, occasionally Kaliyo. Temple gets used the least because her voice, too, grates on my nerves. High pitched, whiny voices on supposedly grown women - blech.
All my other toons are leveling so they're stuck with a limited number of comps.