Here's a favorite of mine: ShopInIsrael.com
Here are a few personal favorites -- I've either bought from them via the 'net and/or in person at Israeli Vendor Fairs, held by area synagogues:
Silverpoint Judaica
Judaica Jewelry - Elon Moreh
Galilee Silks
Dodo's - The Land of T-Shirts
Gabrieli Hand Weaving
Ahava (also available for sale in select dept. stores)
Moshe Dadon - Microcalligraphy
And if you feel like donating some money to organizations which support Israeli soldiers, here are 2 reputable ones:
She was living in Ann Arbor, Michigan in 1993, and did our ketubah for us.