A lot of these sites seem to be more focused to sales and matrimonial listings. I think my site covers the basics, but if you wade around in the mess of these sites, you might find something useful.
Puja - Guide for Educators. This is put out by the Smithsonian Institution in Washington, DC.
Everyday Prayers for Indian Gods. This is a lovely website with English transliterations and translations. The prayers are grouped by day of the week.
Portland Hindu Temple. This website has English transliterations and translations of shlokas as well.
Urday. This site is very interesting to wander around, has a lot of information on Hinduism in general. Does not really have shlokas or image files, though.
Sulekha.com. This site is some sort of Indian gateway. Doesn't have any prayers, but it does have some interesting theological discussions. Worth a look around.
Vaishnodevi Mandir in Jammu. Good site if you want to visit Vaishnodevi or learn about the legend of Vaishnodevi. If you look under "Holy Shrine" and then "Aarti", you will find a list of transliterated shlokas for Mataji.
TempleNet. If you are interested in visiting a Hindu temple, this site has a lot of centralized information and background on the temples.
Bhaktisangeet. This site has images, calendars, transliterated prayers, and more.
An Easy Guide to Indian Culture and Cuisine.
HinduNet. This website has a lot of shlokas transliterated as well.
Online Panchangam. Has transliterated shlokas as well as audio to learn to speak them correctly. This site explains things clearly and has some nice recipes as well.
Vaishnav Community Online. Lots of transliterated shlokas here, as well as audio.
Vedanta Mission. They have an online Gita course. They have prayers, but not transliterated. So you have to read hindi if you want to say them. They have an almanac listing the important religious days on their website as well.
Ambaa South Indian Website. Nothing transliterated, sadly. Great website, though. Lovely images as well.
Durga Puja. This website is lovely, but very slow to load. Transliterated and translated aartis and bhajans.
Sword of Truth's Devi Durga Page. I have no idea who these people are, but they do have transliterated and translated prayers on their website.
Shloka Online. This site has the hindi, english transliteration, english translation and short explanation. It even has the audio for the shlokas. A very good site. Unfortunately, it is limited in the number of shlokas it has.
Archaka Puja Page. This website has transliterated and translated prayers. Also links to a bhajan site.
Balagokulum. Seems to be a kid's site. I can't make the fonts work, though.
Dvaita. This is a nice site. It has some stotras in Hindi, not English. Their pdf files of the stotras are nice.
Astro Jyoti. This website has lovely explanations, translations and transliterations of Sanskrit shlokas and mantras. Definitely check out this site.
Anita's Cuisine. What to eat when you are fasting. Recipe Site. Really yummy.
These are the extent of my links. Honestly, my web site was started because I had such a hard time finding transliterated prayers. I do read Hindi and Sanskrit, just not well. I prefer to read my prayers in English.
I also was trying to hunt down transliterated versions of Mataji prayers so that I wouldn't have to sit there and go through our prayer book and make it my homework to transliterate it. Plus I really wanted the translations to the prayers as well.
Hopefully this site meets that need for others in my position.
If you know of any good sites that I have missed, or are able to translate one of my untranslated prayers (like "Jaya Adya Shakti"), please email me at swdesai21 at yahoo dot come to let me know.