Psychoslice: before you go and read things written by ignorant alarmists I would highly advise looking at source materials Pretty much all of the issues addressed on that website are addressed by the sages in the Gemara. I'll discuss them in general terms here and if you would like me to quote some specific examples then please ask and I will search for them.

1) Capital Punishment Crimes
Capital Punishment as a punitive measure was commonplace for eons. Prisons weren't a viable option back then because the people had a difficult enough time supporting themselves and couldn't be expected to support freeloading prisoners. Imprisonment is hardly a perfect solution nowadays either. The prison system has a very low success rate at reforming criminals, it's a burden on taxpayers and it's a weak deterent for crimes. The only reason for using the prison system over capital punishment is if a society is, for some reason, morally opposed to killing bad people - which is a very recent value.
That being said, the Torah proscribes 3 forms of punishment: (1) Death, (2) Fines, (3) Slavery. The most commonly proscribed punishment, Death, is only enacted if it can be proven, beyond a shadow of a doubt, that the person committed a crime knowing full well what he was doing and that he was in his right mind when doing so. Monetary fines were proscribed for material transgressions, such as theft, damages etc. Slavery was proscribed for those who cannot pay fines and for a few other miscellaneous crimes. To be clear, this is a limited slavery that lasts, at the very most, seven years. And it makes a lot more sense to indebt a criminal to a good family that can show a person the error of his ways rather than lock him up with other criminals to teach him how to be a better thief.

If you argue that some of the laws for which the death penalty are proscribed seem strange I would respond that just because you don't understand something doesn't make it wrong. The Sabbath is one of our most holy commandments and there isn't a question in any religious Jew's mind that breaking the Sabbath makes a person worthy of death. The assignment of the death penalty is more as a sign of the severity of the commandment than an actual punishment - such measures must have rarely, if ever, actually been taken.

2) God's Murders for Stupid Reasons
As stated above, just because you don't understand something doesn't make it 'Stupid'. Also keep in mind that the stories in the Torah took place at a crucial time in the development of the nation of Israel and the people back then were, of necessity, held to a higher standard than the people of today. One of the reasons for this is that Kharmic law for Jews runs through the nation as a whole - when one Jew sins all the other Jews are affected. This special connection also runs forward through time - when one person sins all future generations are affected. The pain and suffering of the past 2000 years was an indirect result of the sins of our forefathers and it is every generation's responsibility to not add to the burden and try to fix up what we can. Knowing this, things may become more clear

3) Murdering Children
This whole section is threats and prophecies save one - the murder of the first borns of Egypt. And that one happened after 9 other plagues.

and 4) Miscellaneous Murders.
Yayaya... see above. Just because you don't understand something doesn't make it wrong.