Here are some of my favorite and well-used travel links.
STA Travel: Only for students. Their package deals are a bit pricey for me, but they do offer a lot of coupons/specials that are worth looking into, and their overseas tickets tend to be the cheapest. They're also a good place to buy Eurorail passes and International Student Cards.
Priceline: I LOVE Priceline. I've now ordered 3 flights, a vacation package, and several hotel through them and have gotten great results. My best buys? A $250 round trip ticket to San Fransicso during peak tourist season, a 7 day hotel+flight package in Ireland for $800 total (yes, that was including taxes and fees and EVERYTHING), and a 4 star hotel in Detroit for $45 a night. Their "Name your own price" function is amazing-it takes a little bit of time, and you have to flexible, but you can save a TON of money.
AerLingus: This site is best for Irish flights and vacation packages, but they do offer great travel and flight deals to the rest of Europe as well. I booked my flight/hotel combo to Dublin through them via Priceline and was very, very impressed. For Ireland, they have the cheapest deals hands down.
TravelZoo: They have this fun little email feature called the Top20, which is their 20 best deals of the week. It's a little hard to search for something very specific, but their Caribbean/Mexican deals can't be beat.
Erika's Travel: Erika's is a travel agency based in Grand Rapids. I haven't personally used their services, but my mother swears by them. When I emailed them to compare flight costs to Brazil, they were prompt and curteous.
Unusual Hotels: Okay, so I haven't actually stayed in any of these, but it's fun to dream :)
More to come!