**Updated to add new items from 1.4.2**
This is my revised list of items that I think would be convenient to have, either because it can take awhile to find the items, or because the items themselves are not obtainable/renewable.
I also added items that have the same ID as other items, but are new (specifically jungle and stonebrick blocks)
renewable : added for convenience or consistency
renewable + silk touch : items that require silk touch can still be difficult to acquire due to rarity of the item and rarity of the silk touch enchant (eg. Mycelium)
non-renewable - added for convenience and because the item is limited in quantity (some are significantly more limited than others eg. Dragon Egg vs End Stone)
02 grass (renewable, obtained with silk touch) grass can be created with herbalism, but it will only work on placed blocks. silk touch is required to actually carry grass blocks
Pros: This lets people easily place grass where they want it.
Cons: not very necessary, herbalism can overcome
05:3 jungle planks (renewable)
Pros: Added consistency (since other wood types exist)
Cons: not very rare
06:3 jungle sapling (renewable)
Pros: Added consistency (since other wood types exist)
Cons: not very rare
16 coal ore (non-renewable, silk touch)
Pros: ability to more easily acquire coal ore
Cons: could be used for exploits
17:3 jungle wood (renewable)
Pros: Added consistency (since other wood types exist)
Cons: not very rare
18:3 jungle leaves (renewable)
Pros: Added consistency (since other wood types exist)
Cons: not very rare
21 lapis lazuli ore (non-renewable, silk touch)
Pros: ability to more easily acquire lapis lazuli ore
Cons: could be used for exploits
30 cobweb (non-renewable, can be only be acquired with high level excavation)
Pros: this item has a lot of fun uses, but is very difficult to acquire
Cons: adding this to the shop kind of takes away the rarity and value of the high excavation required to get it
56 diamond ore (non-renewable, silk touch)
Pros: ability to more easily acquire diamond ore
Cons: could be used for exploits
73 redstone ore (non-renewable, silk touch)
Pros: ability to more easily acquire diamond ore, also would make for really cool paths that light up as you walk over them!
Cons: could be used for exploits
79 ice (renewable, requires silk touch)
Pros: saves on needing to require silk touch, allows people to build larger icy structures
Cons: large icy structures could melt and cause lag
98:2 cracked stone brick (non-renewable)
Pros: make a rare item more obtainable for people to build with
Cons: makes the item less rare, and therefore lessons the desire/accomplishment associated with using the material
98:3 carved stone brick (non-renewable)
Pros: make a rare item more obtainable for people to build with
Cons: makes the item less rare, and therefore lessons the desire/accomplishment associated with using the material
101 iron bars (renewable)
Pros: consistency with fences and glass panes
Cons: not rare
106 vines (renewable)
Pros: consistency with ladders, makes it easier to acquire (even though it isn't terribly difficult)
Cons: not very rare
107 fence gate (renewable)
Pros: easier to get gates for faster building, consistency with fences
Cons: not rare
110 mycelium (renewable, silk touch, very very rare)
Pros: useful material for growing mushrooms, highly sought after material would be significantly more available to everyone
Cons: will drastically diminish the rarity of the material and therefore lesson the desire/accomplishment associated with using the material
111 lily pad (non-renewable, very common in swamps)
Pros: really awesome item for usage around water, it isn't renewable
Cons: it's not impossible to find, just time consuming
112 nether brick (non-renewable)
Pros: more easily access nether-related building materials safely
Cons: makes the item less rare
113 nether brick fence (non-renewable)
Pros: more easily access nether-related building materials safely
Cons: makes the item less rare
114 nether brick stairs (non-renewable)
Pros: more easily access nether-related building materials safely
Cons: makes the item less rare
121 end stone (non-renewable, obtainable from the end)
Pros: more easily obtain the material without having to go to the end
Cons: makes the item less rare
122 dragon egg (non-renewable, there can only be one)
Pros: decoration. there's only one in a vanilla server
Cons: makes the item drastically less rare, and therefore not valuable.
129 emerald ore (non-renewable, silk touch)
Pros: ability to more easily acquire diamond ore
Cons: could be used for exploits
138 beacon (non-renewable)
Pros: more easily access a very rare item
Cons: makes the item drastically less rare and desirable
139:0 cobble wall (renewable)
Pros: consistency with other fences
Cons: not rare
145:0 anvil (renewable)
Pros: consistency with other work-related blocks (eg. workbench)
Cons: not rare
302 chain helm (renewable)
Pros: more easily access rare armor
Cons: makes the item less rare
303 chain chest (renewable)
Pros: more easily access rare armor
Cons: makes the item less rare
304 chain legs (renewable)
Pros: more easily access rare armor
Cons: makes the item less rare
305 chain boots (renewable)
Pros: more easily access rare armor
Cons: makes the item less rare
326 bucket of water (renewable) this is for convenience
Pros: convenience of getting water when it's not around
Cons: not rare
327 bucket of lava (non-renewable) I'm only adding this to have it on the list, I don't actually want this item in the shop. Lava has very limited uses (for making obsidian)
Pros: consistency with bucket of water.
Cons: it's lava. no one actually likes lava. having easy access to such a horrible material could be a very bad decision.
354 cake (renewable)
Pros: cake is a pain to make
Cons: it's a food item
369 blaze rod (renewable)
Pros: easier to acquire
Cons: allows more people to gain access to potions and wreak havoc
370 ghast tear (renewable)
Pros: easier to acquire
Cons: makes it too easy to obtain powerful potions
372 nether wart (renewable)
Pros: easier to acquire
Cons: makes it too easy to obtain potions
375 spider eye (renewable)
Pros: easier to acquire
Cons: could be abused with monster spawners
384 bottle o' enchanting (renewable)
Pros: easier to acquire, would make for a very good money sink for rich players
Cons: makes it too easy to gain access to powerful enchants
388 emerald (renewable)
Pros: easier to acquire
Cons: could drastically affect the economy and shop for awhile. (depending on price)
390 flower pot (non-renewable)
Pros: easier to acquire
Cons: makes the item less rare
391 carrots (renewable)
Pros: easier to acquire
Cons: it's a food item and component for potions
392 potatoes (renewable)
Pros: easier to acquire
Cons: it's a food item
397:0 skeleton head (renewable)
Pros: easier to acquire
Cons: makes the item much less rare
397:1 wither skeleton head (renewable)
Pros: easier to acquire, would allow for players to more easily summon the wither
Cons: makes the item much less rare. rampant withers could be devastating to towns and spawn. super easy griefing tool
397:2 zombie head (renewable)
Pros: easier to acquire
Cons: makes the item much less rare
397:3 player head (renewable)
Pros: easier to acquire
Cons: not too rare
397:4 creeper head (renewable)
Pros: easier to acquire
Cons: makes the item less rare