Search Engine penalize a site if your site have following :
duplicate content
bad neighbour linking
spamming
When google penalize a particular site, often
PR goes to 0. Home page will affect first and slowly the effect gets applied to whole site pages.
To avoid penelization Remeber do not link to a site which has got banned / penelized by SEs. If you have a link partener whose site is having PR0, and you have inbound link from them. Then there is no point in having such a backlink.
Also DO NOT link to a site in link farm, it will cause you penelization.
Also some on-page optimization can lead to penelization. like the tactics heavy keyword repetations in title and in body text. NO Html Validation.
Also you can check the cache for your site. It will show you the last date when crawler crawled your site.
If your site has been penelized it will not see in the SERPs.
Also you will not find any information in site:domain-name.com
Imortant Note :-
New site dont have
PR at starting. They take some days even months to get
PR.
Thanks