This is a Shaymin set that I've been using lately. I think it's relatively decent, so I decided to try posting it; the only set I saw utilizing Substitute was the SubSeed set on the analysis page. I suck at EV spreads, however, so any suggestions would be appreciated.
http://www.smogon.com/dp/pokemon/shaymin
[SET]
name: Substitute + 3 Attacks
move 1: Substitute
move 2: Seed Flare
move 3: Earth Power
move 4: Hidden Power Fire / Hidden Power Ice
item: Leftovers
ability: Natural Cure
nature: Timid
evs: 252 SpA / 4 SpD / 252 Spe
Why this set deserves to be on-site:
- Retains Shaymin's ability to switch in to and threaten bulky Waters, while taking advantage of switches by setting up a Substitute.
- Able to take down Fire-types, such as Heatran and Infernape that would usually cause problems for it.
Additional Comments:
- Hidden Power Fire prevents Steel-types from walling you, and is useful for hitting Skarmory, who could otherwise set up hazards. Hidden Power Ice is used to OHKO Dragonite after Stealth Rock.
- 252/252 for maximum power and the ability to tie with other Base 100's.
- 224 Speed EVs can be used if Hidden Power Fire (results in imperfect Speed IV) is chosen to outspeed Base 95's.
Teammates and Counters:
- Teammates: Pokemon that benefit from the removal of Fire-types, and to a lesser extent, threats that are hit by the Hidden Power type chosen. Some examples include Jirachi, Scizor, and most other Steels.
- Counters: Blissey is a 100% counter to this set, but switching out while still behind the Substitute could allow you to bring in a sweeper without being statused. Snorlax also counters the set.

http://www.smogon.com/dp/pokemon/shaymin
[SET]
name: Substitute + 3 Attacks
move 1: Substitute
move 2: Seed Flare
move 3: Earth Power
move 4: Hidden Power Fire / Hidden Power Ice
item: Leftovers
ability: Natural Cure
nature: Timid
evs: 252 SpA / 4 SpD / 252 Spe
Why this set deserves to be on-site:
- Retains Shaymin's ability to switch in to and threaten bulky Waters, while taking advantage of switches by setting up a Substitute.
- Able to take down Fire-types, such as Heatran and Infernape that would usually cause problems for it.
Additional Comments:
- Hidden Power Fire prevents Steel-types from walling you, and is useful for hitting Skarmory, who could otherwise set up hazards. Hidden Power Ice is used to OHKO Dragonite after Stealth Rock.
- 252/252 for maximum power and the ability to tie with other Base 100's.
- 224 Speed EVs can be used if Hidden Power Fire (results in imperfect Speed IV) is chosen to outspeed Base 95's.
Teammates and Counters:
- Teammates: Pokemon that benefit from the removal of Fire-types, and to a lesser extent, threats that are hit by the Hidden Power type chosen. Some examples include Jirachi, Scizor, and most other Steels.
- Counters: Blissey is a 100% counter to this set, but switching out while still behind the Substitute could allow you to bring in a sweeper without being statused. Snorlax also counters the set.