For me, it's Julan and Constance. They just seem a good all-around combination. But I'm interested to hear what other companions people are using.
I use Julan and Constance too. I've only tried the Julan Romance option once and didn't care much for it. I suggested to Kateri the idea of the PC matchmaking for Julan and Shani but she didn't like the idea. Oh well...
Julan's pithy commentaries (especially his thumbnail book reviews) and his loyalty, in spite of his mood swings make him a joy to have around.
I've used Constance a half-dozen times and she still can surprise me. The last time I used her she gave a passionate anti-slavery speech I never saw before. I didn't think she had a political pixel in her body.
Before I started using companion mods my chars tended to feel depressed after finishing the MW and Tribunal Main Quests (but that's another story.) Companions add friendship and support that you don't find enough of in the Morrowind world.
I'm trying to use Jasmine but I keep getting so many glitches that I'm totally frustrated.