Hi all,
I am planning a trip this coming summer to Japan.

My itinerary is as follows:

3 nights in Kyoto.Hotel Granvia Kyoto.
2 nights in Hakone.Hotel Fujiya
4 nights in Tokyo.Park Hotel.

I am trying to assemble the trip on my own and I'd like to maximize my budget.So I have a few questions regarding hotel reservations.

The best rates for both Kyoto and Tokyo I found them at Agoda.com.Is there any other website to get better rates?

Thanks in advance.

I did try Agoda.com and gave me

The best rates are almost always found on the hotel's Japanese language website. I have never found that any booking site beats the hotel's own rates. Thing is, the hotel's English language website does not usually list the many package and promotional rates. If you can navigate in Japanese and/or use an online translation tool, you can see for yourself. Another benefit is that many more room types are usually available to choose from than in English or on booking sites. And you do not have to pay in advance, or even give a credit card number, in most cases.

Exceptions are big international chains like Hilton, luxury brands like Peninsula and Mandarin Oriental, and perhaps hotels that cater to foreigners, like the Fujiya in Hakone.

I usually ask someone in our Tokyo office and I think she uses a website (or could be a travel agent?) named Jalan. Unfortunately all is in Japanese--maybe if you know someone who reads Japanese he/she can help? I print out email confirmation (comes in Japanese) just to be safe, but never had troubles with the reservation.

Jalan is a hotel booking site run by Recruit (mainly a recruitment company). There are several other popular online sites, such as Rakuten (run by an online virtual shopping site; simplified version available in English, but Japanese version is much more comprehensive), and major tour operator/travel agency like JTB and Nippon Travel.
You tend to get very similar rates across booking sites, but as availability differs (depending on each site's room allocation), it's worth going throug as many as you can (if you read Japanese), esp at peak periods.
But I agree with KimJapan that the hotel's own Japanese website usually gives the best rates and choices - some guarantee they beat any other online quotation!

Thanks a lot, that was quite helpful.