We use Itranslator for typing Sanskrit. Developed at Omkarananda Ashram in Rishikesh, along with a beautiful Sanskrit font called Sanskrit 2003, the program converts text entered in “itrans” format (using a standard keyboard) into Devanagari and standard transliteration. For example, “OM namaH shivAya” will convert to “ॐ नमः शिवाय” and “om namaḥ śivāya”. The Sanskrit 2003 font contains hundreds of conjunct forms, for good rendering of Sanskrit. The program and font can be downloaded here free of charge.
For typing Bengali, we have found the Rupali keyboard layout to be easy to learn, as it matches the English keyboard where possible. It can be downloaded free of charge. Very few Bengali fonts contain the avagraha character, which is needed for proper writing of Sanskrit. One of them is BenSen, which can be downloaded here.
We have found a very useful website which can transliterate from one Indic script to another. We use it especially to render Sanskrit hymns in Bengali script. Some minor proofreading is required, to add ওঁ (om) and to convert য to য় where needed (“ja” to “ya”).
Update: this site seems to have folded. Another site for inter-script transliteration is here.