I'm in the market for a new taco...

Looking at pricing what should I get vs. avoid getting from the dearler.

1) Security system
2) Cap
3) Skid plate
4) running boards
5) dimming mirror

Spot

I will just put in my opinion on this one. 1) If you need it get the security system, I guess it depends where you live and how worried you are about a break in. I don't know how the system compares with aftermarket but I also don't know how different systems are in general. 2) Cap as in shell? Shells are nice and if you can get it for a good deal with the sale then that would be good. They might overprice it when they add it though so you will have to compare the price they would add to what a new one would be. 3) The stock skid plate isnt bad, I have railed mine of many rocks and it is holding up. Eventually I think I will get a different one but stock they are alright. 4) From what I know I think the running boards that would come factory are worthless. They are nothing like rock sliders and dont really do much for you. 5) Dont know what you mean by dimming mirrors.
That is my two cents.

1) Security system - Aftermarket
2) Cap - Aftermarket
3) Skid plate - Depends how tough you plan on being.
4) running boards - Have em, hate em, wouldn't have gotten them if I didn't like the rest of the truck. Although they do block a lot of debris from chipping the lower paint.
5) dimming mirror - Not for me since I always tint the windows, but I would get factory if I wanted it.

I would have bought the cap from the dealer if I could do it all over again. I could have gotten the Snugtop for ~$1500 with the truck and could only find it for $1800 thereafter - even from the same dealer. (yeah, that makes no sense, but it is true.) I ended up with the ARE Z-series for $1600. If you don't want to spend that kind of money, there are definitely cheaper options for metal as apposed to fiberglass. Not sure if the dealers handle anything other than the Snugtop - it seemed like there was some kind of agreement between Toyota and Snugtop.

I'd get the cap and that's about it...

If you get the cap, make sure you DON'T buy the TRD Sport. The rear springs are soft and sag easily to begin with let alone putting 200 lbs. of fiberglass on the bed.

The fancy bling skid just looks good IMHO (I guess sort of like my hood scoop.)