So you want the beginnings of a reef, are you going to want soft corals, LPS or SPS dominate tank?
You forgot lighting.
Overflow, forget it. If you don't have the tank buy a reef ready. It is $150 more than the cost of a plain tank but that's about what you'd spend on an overflow box and accessories.
Protein skimmer. If you want to do it right the first time buy a Deltec. I understand they are very expensive so a good alternative is Euroreef. ER is exclusively what I run. One of mine would retail at $7,500 (5' tall with 4 Eheim modded pumps.), I also have what is now the RS80 and an RC135. The RC line is expensive but worth it. Next up would be ASM. Check Ebay as the prices are right. Be careful about the pricing. The ASM G1 might be $200 but the G3 might only be $265. If you have the room the G3 would be a better value. I've seen an Octopus ASM clone that was of decent quality. The owner said it was very nice, I believe him. Basically ASM and Octopus are ER clones made with less quality materials. Octopus also has a recirculating skimmer. If you type in ASM in a search engine an old shop that called themselves ASMonline now exclusively sells the Octopus line.
Sump. I really like my Trigger Fish System Berlin sump/fuge combo. It retails for about $450.
http://www.premiumaquatics.com/Merch...y_Code=CprSump 
However you can make an efficient set up from an old tank such as a 30 or 40g. Esumps also sold as Eshoppes, is another decent choice.
Do you need one? If you want to hide all your equipment they are nice, plus they add a few more gallons to your total water volume. The falling water naturally respirates, exhaling toxic gases and inhaling oxygen. The falling water mixing with O2 also cools the water up to 3 or more degrees.
Return pumps, nothing beats an Eheim for in sump. Hands down the finest, quietest, coolest running and most efficient. Mag drives hold nothing on Eheim. For a 40-50g I'd look into a 1260 possibly 1262.
Circulation, I'd get Tunze Turbelle Streams like the 6060 or a surging model like the 6100, better yet is the Tunze Wavebox. But you could save several hundred dollars with Hydor Korallia stream pumps. Stream pumps are the way to go.
Lighting. The stock lighting will never do. Plenty of T5 bulbs, As many as will fit your tank with Tek2 reflectors from Sunlight Supply or possibly 2 smaller halides of about 70-175w each of about 12-14K and 2 T12 VHO super actinics from URI for growth and color. The T5's would be great if you keep softies and some LPS. You'd want the halides if you get into SPS corals.
Of course these are only suggestions and you can put together a tank hundreds of different ways. What I mentioned are the hobby staples for reliability, ease of use, quiet operation, low heat, low maintenance, no headache products. You could even do it all one better by buying a good controller like an Aqua JR. controller or ReefKeeper II. These are the suggestions based upon what I use, have used, or know being used. There are other products of lesser and better quality, lesser quality products tend to cause irritation and the possible disappointment in the hobby.
