So I've joined a few guilds in Skyrim and completed there quests and became leader of said guilds. But my question is what are the perks for becoming a leader of guilds what do you get?

Armour for thieves, axe for warriors, blade of woe for brotherhood, robes for mages, as well as a spiffy room.

Rewards:
- Companions: Wuuthrad, and Shield of Ysgramor
- College of Winterhold: Arch-Mage Robes and a Fancy Room
- Bards College: Nothing Special
- Blades: Induct 3 New Members Into The Blades; Go Dragon Hunting With The New Members!
- Dark Brotherhood: Blade of Woe and Dawnstar Sanctuary Master Bedroom
- Imperial Legion: Legate Rank
- Stormcloak: Stormblade Rank

stormblade ain't a rank, it's a title

You forgot a few:
Companions-Harbinger's room (and all its contents)
Blades-Potion that decreases dragon damage (bugged apparently).
Dark Brotherhood-Initiate companions.
Thieves Guild-Guild Master's Armor and a Tribute Chest.

Also, because of the pacing of the MQ in the guilds one tends to miss out on the side quests of the guild. Talk to the various members and see if there is work. I know as the leader the rank and file should not be telling you what to do, but it does lead to some neat quests. I call them the jobs that were too tough for anyone else to do to get around the issue.

I usually enjoyed the side quests more than the stages in the MQ, although there is not as much of a story.

When your named Harbinger and get Kodlak's old room, I know the "stolen" tags are removed from everything. But is the storage safe?

I don't think so but don't quote me on that.

I know the display cases reset after a period of time though.

I thought they did re-set so have not risked it. Thats what Honeyside is for.