The stiff backbones of conjugated polymers can lead to a rich phase behavior that includes both crystalline and liquid crystalline phases, making measurements of the glass transition challenging. In this work, the glass transitions of regioregular poly(3-hexylthiophene-2,5-diyl) (RR P3HT), regiorandom (RRa) P3HT, and poly((9,9-bis(2-octyl)-fluorene-2,7-diyl)-alt-(4,7-di(thiophene-2-yl)-2,1,3-benzothiadiazole)-5′,5″-diyl) (PFTBT) are probed by linear viscoelastic measurements as a function of molecular weight. We find two glass transition temperatures (Tg's) for both RR and RRa P3HT and one for PFTBT. The higher Tg, Tα, is associated with the backbone segmental motion and depends on the molecular weight, such that the Flory-Fox model yields Tα = 22 and 6 °C in the long chain limit for RR and RRa P3HT, respectively. For RR P3HT, a different molecular weight dependence of Tα is seen below Mn = 14 kg/mol, suggesting this is the typical molecular weight of intercrystal tie chains. The lower Tg (TαPE ≈ -100 °C) is associated with the side chains and is independent of molecular weight. RRa P3HT exhibits a lower Tα and higher TαPE than RR P3HT, possibly due to a different degree of nanophase separation between the side chains and the backbones. In contrast, PFTBT only exhibits one Tg above -120 °C, at 144 °C in the long chain limit.