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Hi,
I recommend to use the freely available (copyrighted) EPA EPI suite:

It contains some 103.000 structures + CAS numbers (SMILECAS database)
and (PHYSPROP database) with around  25,000 compounds with
experimental data (logP, bp, henry..) and you can also calculate
a lot of physico-chemical properties.

Instead of repeating all the important things from
http://www.epa.gov/opptintr/exposure/docs/episuite.htm
I will pick out some things:

   AOPWIN - estimates atmospheric oxidation rates
   BCFWIN - estimates bioconcentration factor (BCF)
   BIOWIN - estimates biodegradation probability
   ECOSAR - estimates aquatic toxicity (LD50, LC50)
   HENRYWIN - estimates Henry’s law constant
   HYDROWIN - estimates aqueous hydrolysis rates (acid-, base-catalyzed)

   KOWWIN - estimates octanol-water partition coefficient
   MPBPWIN - estimates melting point, boiling point, and vapor pressure
   PCKOCWIN - estimates soil sorption coefficient (Koc)
   WSKOWWIN - estimates water solubility
   DERMWIN -  Dermal Permeability Program
   STPWIN - (Sewage Treatment Plant Fugacity Model)
   WVOLWIN - (Volatilization Rate from Water)
   LEVEL3NT - (Level III Fugacity Model)

* EPIWIN allows batch file input for a large number of compounds

* MPBWIN has an experimental database of
11347 compounds (8948 melting points, 6381 boiling points,
and 2857 vapor pressures) - this may be useful for retention time
fitting (assuming same class of compounds).

* KowWIN - contains a database of 13200 experimental log P values.
and also a algorithm for calculating unknowns via smiles structure
input.
(Please take care: blind usage of calculated logP values is like walking
in a mine field:-)
further reading: http://www.lnh.unil.ch/Appl/cchem2.html
and http://esc.syrres.com/interkow/kowdemo.htm

* I also recommend to read:
Identifying Unknowns with “Spectraless” Databases from James Little
http://users.chartertn.net/slittle/files\TSCA_Poster%20Session.pdf
from http://users.chartertn.net/slittle/tsca.html
because it gives some important hints how mass spectra and mol masses
and databases can be linked together.

* Some rare EPIWIN examples for testing
Consul : (CAS 86479-06-3)
Fc1cccc(F)c1C(=O)NC(=O)Nc2cc(Cl)c(OC(F)(F)C(F)F)c(Cl)c2
Transfluthrin: (CAS 118712-89-3)
Fc1c(F)cc(F)c(F)c1COC(=O)C2C(C)(C)C2C=C(Cl)Cl


With kind regards
Tobias Kind

PS: Thanks to U.S.EPA Office of Pollution Prevention Toxics
and Syracuse Research Corporation (SRC) and ...

PPS: Try  the incredible CACTVS system at
http://www2.ccc.uni-erlangen.de/ncidb2
It has enhanced features now - this is truly a state-of-the-art "open
database concept"
it has dozen of (multiple) input and output options. Try molsurf and
orbvis!

PPPS: Most molecular editors and some java applets import and export
smiles.
If you have a CAS number you can now use SMILECAS or CHEMIDplus - later
Merlin or ISIS/Base or whatyouwant for a structural
similarity/substructure search.
After data retrieval you can search with the obtained structures
for similiar mass spectra or substructures using NIST MS search V2.0
http://www.nist.gov/srd/nist1a.htm

PPPPS: if you want more information about PPPS you should change
to news:sci.techniques.mass-spec (without any additional cost:-)