What do most places do when it comes to a tune up?
Plugs
Fuel filter
Change oil
Make misc adjustments

All has to do with what you want. I would ask for platinum plugs, new coil boots, throttle body cleaning, maf cleaning, fuel filter, and air filter. If it's due an oil change then so, etc. That's what I've done myself on my 97. The 06 I paid someone else to do. With my old back and arthritis I will pay someone to do it again.

Just about anything to improve my mileage somewhat and make it run a tad better. I know 150,000 miles on a 5.4 can't be great but any little help I can get would be good.

Oh I forgot replace the pcv valve. Also check the rubber elbo that connects the pcv valve tube to the rear of the throttle body as they have a tendancy to crack. As far as fuel mileage I've done a few things to my 97 and didn't see much improvement, probably 1-1 1/2 mpg at the most but performace wise I did see improvement there. I install a Gryphon tuner with a 87 oct performance, 87 oct tow, and 93 oct performance tunes. The Gryphon is a custom tuned Edge tune which they don't do anymore but you can still get the Edge tuner and it's canned tunes will still work. I put dual exhaust system and did the Gott's Mod air intake over the CA intake. Also removed the silencer in the intake elbo. These were all affordable for me and didn't take away from the OEM appearance. The fun factor improvement was worth the investment as my personal experience.

Link to the Gott's mod.

http://www.fordf150.net/articles/idx.php/0/021/article/Gotts-Intake-Air-Intake-Modification.html

Link to silencer removal

http://www.fordf150.net/howto/airintake.php

You might have a stroke when you get a price to have the Plugs and coil packs replaced. Its a mostly labor because some of them will break even after going by the tsb from Ford. If I had my shop built I would do them for you at a reasonable rate. I do it the 2 day job way.

The 97-03's are not the ones that break the 04-08's are the one's bad about breaking. the 97-03's if the plugs are not torqued to at least 32ft-lbs are prone to launch themselves. I've done my 97 twice myself and outside of nearly needing traction because of the bending and contorting not to mention my arms looking like I was in a fight with a wildcat I wouldn't hesitate to do it again. Now the 06 I have is a different story all together I had it tuned up by a former Ford Master tech that opened his shop in Wylie as he was referred by a friend and it cost a hair less than $400 and that included boot's and a fuel filter. Unless a coil on plug (COP) is bad there isn't a reason to replace them just the boots is all. The guy that did mine said his price factored in breaking three plugs, he actually broke 4 of mine. Believe me I'm not going to wait another 100k to do the next, probably 50-60k which is what I think they are recommending now.