I am about to go on vacation in Israel (the holy land), I am very excited and I am doing a lot of research so I know where to go and what to see. My first stop will be in the holy city if Jerusalem. I'm also planning to visit the dead sea, tel aviv,
Eilat and maybe some northern parts in Israel.
I am looking for a good jerusalem hotel and a good price on
car rental in israel ,
if anyone can suggest any company for car rental or hotel I would be happy to know.
I have also heard about guesthouses in Israel, and that they offer good bed and breakfast deals and are very clean.
If one knows of such a guest house I would love to hear about.

Welcome to TT!
I can't advise you on specific hotels, because I live in Israel and have no use for them myself, but you need to state what sort of budget you have. And not "reasonable" or "inexpensive" because what is reasonable to one person could be outrageously expensive to somebody else. Israel is over-endowed with luxury hotels at very high prices, and there is unfortunately a shortage of low-priced accommodation. That's not to say it can't be found, but you may be shocked at the prices.
As a general rule hotels are cheaper in east (Arab) Jerusalem than west (Jewish) Jerusalem. The facilities may not be so good; I have no personal experience.

I don't know if its too late to plan you trip, but I've been to Israel four or so times and I have found that if your looking for something specific, like a bed and breakfast or cheap car rental, use a travel agency . I live in Philly so my family uses one located near us but I am sure that if you do a simple web search you can I find one located near you. What ever you do though, make sure that the agency you use specializes in Israel . No amount of effort on you part can match the wealth of knowledge held by an experienced agency.