Some things to watch for when buying online...check sponsor forums here - lots of sponsors offer RC members discounts.
Also watch for places that are near you. I live in Wisconsin and can order from either Doctors Foster & Smith or AquaCave and have next-day shipping and just pay ground shipping costs. Some vendors (like AquaCave) offer free shipping if you hit a certain $$$ amount. So for me, I pretty much got free next-day shipping from them.
My list is below. I'm BLOWN AWAY by the service from AquaCave and The Filter Guys. DFS and CustomAquatics are pretty good, but my only issues there are some returns that are taking forever to processs.
What do you get online? What do you get from LFS? What do you get 2nd hand/ebay?
Only my tank/stand/canopy/tops are local. Everything else was bought online
Favorite online Fish stores?
New tank so no fish purchases at all yet - but everyone talks highly of LiveAquaria. Shipping livestock can get expensive, but look on this site for local reefer clubs and see if members need to hop in on an order with you and split shipping that way.
Consider having shipments held at Fed Ex/UPS offices for pickups so they're bouncing around less - and heated better if weather's an issue. Plus depending on your dropoff time, sometimes you can get your critters into your tank MUCH sooner if your schedule allows for you to do pickups.
Favorite online invert stores?
My live rock is from Premium Aquatics - considered Dr.Mac (PacificEastAquaCulture.com)
Favorite online equipment stores? (Tanks/Filtration etc..)
My bigger gear is from CustomAquatics.com, lighting is from AquaCave.com, RO/DI is from TheFilterGuys.biz. If I were to do it again I'd have gotten all my CustomAquatics stuff from AquaCave because I'd have saved $$$ on shipping and AquaCave has awesome service.
Favorite consumable stores? (Food / Test Kits / salt etc...)
My incidentals are from DoctorsFosterAndSmith.com