PFBC is open to suggestions on their homepage. This is your chance to voice your opinions to the guys who can/will make a difference. Get active, and educated. http://fishandboat.com/musky-plan.htm
This is what I had to say:
 
I would like to see the musky fingerlings that currently are stocked to be another 6 months or so in age and stocked in better habitat. In my opinion, these 4-7 inch musky fingerlings are the most perfect little snack baits for bass, walleye, pike, and even musky. With an extra couple of months to get into the 10-15 inch range, the survival rate should be incredibly higher, thus having to stock fewer fish to reach established goals of adult musky populations per acre. I know it is expensive to raise those fish a few extra months and transitioning them from pellets to minnows is tricky, but I think it could be worth it.
To fund raising these fish a few extra months, maybe have anglers pay a 5 dollar per year stamp to be able to keep/harvest muskies. This would force the "average joe fisherman" who might randomly catch one per year to either purchase the stamp in advance, or to release the fish!  Most avid musky fishermen would not have an issue with paying an additional fee for better fishing opportunities.
 Also, I have noticed in many bodies of water that the stocking trucks will dump the musky fingerlings into the "most convenient" locations on the lakes instead of putting in a little extra effort to find them better habitat. There isn’t much cover around or near boat launches and I feel they don’t stand a chance against predators.  So much money is spent raising these fish, at least give them a chance!
I’ve recently heard and seen on the stocking website that the 3 rivers musky club is experimenting on a few N.W. PA kettle lakes, where they are stocking the 10-15 inch yearlings and I am very interested to see how that pans out.  Many mid-west states like Indiana have been implementing this method of fewer but larger fish stocked, and studies have shown much greater success in survival rates of fish reaching adulthood.
In conclusion, I would personally like to see muskies stocked larger and to be stocked in habitat areas where they have a better chance of survival.  This may more expensive, but a musky stamp could cover much of the expenses.  A musky stamp would increase revenue specific for this type of program that most dedicated musky fishermen would accept.  In addition many accidental catches would have to be released if a stamp had not been purchased by a fisherman thereby protecting existing populations.

Boro,
You make so good points and some of those issues are already being addressed.  The Linesville hatchery has been producing fish that are averaging 8-10 inches the past 2 years and ready to stock usually first week in april.  The 3 rivers club has helped a lot by donating money to purchase bait for the fingerlings.  Also the 3 Rivers club has been organizing float stocking efforts to put fish into better habitat.  If you would like to help on waters that you fish then you should contact Joe Houck at the 3 rivers club.  There was recently a meeting at north park lake covering the musky plan and the idea of a musky stamp was brought up.  They didn't sound keen on the idea.  It doesnt hurt to give your opinion though, that's what the comment form is for.  They did mention that last time they did a survey like this that public comment had an impact on raising the size limit to 40" instead of having it lower.

Personally, I think there is too much focus on stocking and not enough on management, angler education, and especially habitat. This isn't specific to muskie, but it definitely applies. 

Concur, think that management and habitat are big issues.  It has been our experience that new 40" limit is having the desired impact--we hoook/catch/release more Musky than ever on the Allegheny now.  IMO, catch n' release now LESS of a concern.  Have to put them back under 40", and most guys w/ standard spin outfit are NOT going to land a 40"+ fish unless fishing by boat in colder weather, and will need a good net man and a little luck.  Most guys who hunt trophy Musky catch/photo/weigh/release. 
 
Education on catch n' release (e.g., keeping them in the water and using pliers to get hook out of corner mouth hook or cutting line if well inside mouth gives fish better chance of survival vs. lifting onto shore or boat, handling and trying to get hook back) can go a long way too. 
 
I have some concerns about the impact that too many 'Alpha Predators' will have on forage in certain lakes and rivers--and am one who wasn't too upset w/ a bunch of 32" Musky being 'culled' so they couldn't gobble up the young Smallies and Walleye. 

Comment deadline was Nov 30, 2012...from my understanding
 
A good balance is needed of stocking, management, habitat management and education alike.  If you've been at this awhile, you know that muskie fishing has come a Hell of a long way from the 70s and 80s.  Often times we forget that and need reminding.  That doesn't mean it stops there though, continued efforts are needed as well as recruiting/educating the youth to become supporters and advocates to the sport and its well being.  
 
I also remember back in the day the PFBC would rarely work with the public and/or concerned anglers.  Certainly something to be said for their efforts and work with anglers today to help ensure a good future of the sport.  I suggest if you have genuine concerns, to join a club like 3 Rivers Muskies Inc. chapter and get involved....They are your number one avenue to get connected with the PFBC since they are currently working together on raising bait and stocking of  more mature muskies in the the state.

In late May this year, a buddy of mine and myself were at woodcok* spillway, and witnessed 6 younger males (about18-20 years old) fishing for muskies using a size 2 treble hook with a tiny red-worm. They caught 8. All of which were snagged between the lower jaw and the pectoral fins. It was ridiculous and got me so fired up. When they would bring the fish to shore, several were dropped on and in the rocks, they'd bring the fish up into the grass and gravel while de-hooking and letting them flop all over. and basically drop them over the fence while releasing.  On average, these fish were out of the water for 3-5 minutes. By the end of the day, 2 were dead laying on the bottom. Due to poor cell phone service, i could not call the fish and boat and report it. 2 of which did not have licenses as well.  I probably will never return there b/c of how many times I have seen this kind of stuff happen there. Something should be done. But what?

^I have seen that there before too, very sad.  While reading "several were dropped on and in the rocks, they'd bring the fish up into the grass and gravel while de-hooking and letting them flop all over" I was picturing the times I've seen it there.  Makes me angry everytime I think about it. People like that shouldn't be allowed to fish ever. I truly believe the PFBC should have some sort of test regarding fish handling when you go to buy your license.  I highly doubt it will end all the bad handling, but at least it's a step in the right direction. 

There was a great article on stocking in the midwest in a recent issue of Musky Hunter. It went into great detail on stocking size and compared fish reared on minnows and pellets. Very interesting. Fish raised to slightly larger sizes on minnows had an incredible survival rate. Pellet heads are the lowest of the low. Pond raised fish were also superior to fish raised in concrete race ways.
I think there is just not enough interest to have a viable musky stamp program. What they need to do is drop the trout stamp and up the price of the license as a whole every year for more programs.
Lets face it, the fish commission needs to be completely revamped. They have been top heavy for a long time and are very mismanaged. They need to look to new technology for the fish they do raise. In my opinion they should never have to eliminate entire hatcheries of fish because of disease. If we improved habitat for natural reproduction in PA we wouldn't have to spend as much on stocking.

How about stamps to keep/harvest the fish.... I havent kept a trout in 15 years, why should i pay the same amount for a trout stamp as people who keep 20-30 per year? If no one kept them, they wouldnt have to raise/stock as many, thus saving tons of money that can be spent elsewhere. Same with other species
 

i think conditions and pressure have more to do with the musky fishing than anything...you put junk in the water it affects them"weed killer,invasive species,ect"...you pound lures on small waters they get conditioned not to hit.
i geuss this is the rantings and ravings of a musky fisherman...woe is me...haha
 
I like slot limit sizes. some people eat these stinky rockets.