We combine the Ly- \alpha forest power spectrum ( LYA ) from the Sloan Digital Sky Survey ( SDSS ) and high resolution spectra with cosmic microwave background ( CMB ) including 3-year WMAP , and supernovae ( SN ) and galaxy clustering constraints to derive new constraints on cosmological parameters . The existing LYA power spectrum analysis is supplemented by constraints on the mean flux decrement derived using a principle component analysis for quasar continua , which improves the LYA constraints on the linear power . We find some tension between the WMAP3 and LYA power spectrum amplitudes , at the \sim 2 \sigma level , which is partially alleviated by the inclusion of other observations : we find \sigma _ { 8 } = 0.85 \pm 0.02 compared to \sigma _ { 8 } = 0.80 \pm 0.03 without LYA . For the slope we find n _ { s } = 0.965 \pm 0.012 . We find no evidence for the running of the spectral index in the combined analysis , { dn / d \ln k } = - ( 1.5 \pm 1.2 ) \times 10 ^ { -2 } , in agreement with inflation . The limits on the sum of neutrino masses are significantly improved : \sum m _ { \nu } < 0.17 eV at 95 % ( < 0.32 eV at 99.9 % ) . This result , when combined with atmospheric and solar neutrino mixing constraints , requires that the neutrino masses can not be degenerate , m _ { 3 } / m _ { 1 } > 1.3 ( 95 % c.l . ) . Assuming a thermalized fourth neutrino we find m _ { s } < 0.26 eV at 95 % c.l . and such neutrino can not be an explanation for the LSND results . In the limits of massless neutrinos we obtain the effective number of neutrinos N _ { \nu } ^ { eff } = 5.3 ^ { +0.4 } _ { -0.6 } { } ^ { +2.1 } { } _ { -1.7 } { } ^ { +3.8 } { } _ { -2.5 } and N _ { \nu } ^ { eff } = 3.04 is allowed only at 2.4 sigma . The constraint on the dark energy equation of state is w = -1.04 \pm 0.06 . The constraint on curvature is \Omega _ { k } = -0.003 \pm 0.006 . Cosmic strings limits are G \mu < 2.3 \times 10 ^ { -7 } at 95 % c.l . and correlated isocurvature models are also tightly constrained .