In what buffer can we store few megabase size chromosomal DNA: TE, Tris or DW? and for how long can we store at -20 degree without significant degradation.

The number of times a DNA sample is freezed thawed tends to be far more important than whether it is stored in TE or water. If you're storing it long term as an archive for possible use at a much later stage, personally I'd choose TE but have no real evidence for that choice. If you are going to access the DNA lots of times, I think it's far more important to freeze it in small amounts.

In agreement with labrat, your DNA samples will be damaged as you continue to freeze/thaw them. Minimize this if at all possible.

If not, you can check for damage by using a DNA Damage ELISA Kit which detects 8-hydroxy-2-deoxyguanosine (8-OHdG). 8-OHdG is a biomarker for oxidative damage to DNA. Stressgen Bioreagents Corp sells a kit for this purpose.

Then, if you need to repair your DNA sample, you might want to look into the Auroris PCR Repair Kit manufactured by Q-Biogene.

I do not have any performance information on either of these kits, but they seem like something that might be useful to you.

QBiogene used to make the DNA repair kit you suggest but they've discontinued it. Any suggestions on where to find something comparable?

Biocompare.com has lots of information comparing kits. They would likely have information on other kits of that type.