The Rules:
No two programs of the same colour can touch, or error will occur.
Program (clear) parts must have at least one block on the memory line
Plus with a square pattern) parts must not touch the line

However, all the above rules can be made redundant by equpping the BugStop program, which gets rid of any bugs. ^^ Until you get that though, pay attention. When you try and run the programs, MegaMan will feel funny if you've made a mistake.

Certain programs can only be equipped by certain styles. If you try and equip a green program while in the Guts style, it will come up with an error message. We'll get to that in the third section.

Programs

Alpha		Can see puddles of Alpha on floors of WWW Comps	All	An e-mail from Dad
AntiDmg		When hit, B and left hurls throwing star at enemy	Guts Shadow	Shadow Style level 4
Atk1		Uncharged Megabuster goes 1 extra damage	All	Beach Square program shop
Atk1		Uncharged Megabuster goes 1 extra damage	All	Start with one, DDN 2nd floor security panel
Atk1		Uncharged Megabuster goes 1 extra damage	All	Hosp Comp 2
Battery		Electric-type viruses attack more often	All	Under Square program shop
Beat		Take hugh level chips from defeated opponent (Link battles only)	All	Under Square program shop
BlckMind		Allows you to freely access Undernet.	All	Chaud in Virus lab as part of storyline
Block		When B and left is pressed, only half damage is inflicted	Custom Shield	Shield Style level 2
BrakBust		MegaBuster goes through guards	Guts Shadow	Guts Style level 4
BrakChrg		Powered Megabuster attack goes through guards	All	The black man in DNN building
BrakChrg		Powered Megabuster attack goes through guards	Guts Shadow	Guts Style level 3
BugStop		Stops bugs occuring in Customiser	All	Bug Style level 2
BustrMAX		Megabuster abilities are maxed out	All	Undernet 6 BugFrag shop
Charge1		Megabuster charges faster	All	Beach Square program shop
Charge1		Megabuster charges faster	All	Zoo Comp 2, Beach 1, and start with one
Charge1		Megabuster charges faster	All	Hosp COmp 5
Collect		More chance of defeated enemies dropping chips	All	Hidden console in WWW base (go up from the boat and it's begind a wall)
Custom1		Can choose one more chip in battles	All	Custom Style level 3
Custom1		Can choose one more chip in battles	Custom Shield	Custom Style level 2
Custom2		Can choose two more chips in battles	Custom Shield	Custom Style level 4
DarkLncs		Don't need to have a hole in battlefield to use chips that need it (i.e. OldWood)	Requires erorr code	Bug Style level 3
EngyChng		Allows you to burn the tress in Hosp Comps and put out the fires in Cyberworld (PlantMan and FlamMan sections)	All	Hosp Comp 1 (storyline)
Fish		Water-type viruses attack more often	All	Beach Square program shop
FlotShoe		Panels types have no effect	Guts Shadow	Shadow Style level 3
FstGauge		Custom Gauge fills faster	All	NumberMan code
GigFldr1		Allows one extra GigaChip in folder	Requires error code	Undernet 7
HP100		Adds 100HP to MegaMan	All	DNN Van, Undernet 6 BugFrag shop
HP100		Adds 100HP to MegaMan	All	Zoo Comp 4
HP200		Adds 200HP to MegaMan	All	Undernet 1
HP200		Adds 200HP to MegaMan	All	Undernet 6 BugFrag shop
HP300		Adds 300HP to MegaMan	All	Under Square program shop
HP500		Adds 500HP to MegaMan	All	Secret Area 2
HubBatc		Has effect of following programs: SprArmor, BaekBust, BrakChrg, Custom1, MegFldr1, AirShoes, FlotShoes, ShdwShoes, and Shield. Also causes a glitch that cuts your HP in half, but this can be stopped  with BugStopper.	Requires erorr code	Secret Area 3 (link)
Humour		When in real world press L button for MegaMan to tell a joke	All	Job 16
Jungle		Wood-type viruses attack more often	All	WWW Comp 3
MegFldr1		Allows one extra MegaChip in folder	All	Team Style level 3
MegFldr1		Allows one extra MegaChip in folder	Ground Team	Team Style level 2
MegFldr2		Allows two extra MegaChips in folder	Ground Team	Team Style level 4
OilBody		Fire-type viruses attack more often	All	Hosp Comp 1
Press		MegaMan can walk across the thin walkways	All	Dr Cossack (storyline)
Reflect		When B and left is pressed, attack is reflected back	Custom Shield	Shield Style level 4
Reg5		Increases regular memory by 5	All	Beach Square program shop
Reg5		Increases regular memory by 5	All	Undernet 6 BugFrag shop
Rush		FInd invisible opponents (Link battles only)	All	Undernet 6 BugFrag shop
SetGreen		Changes panels to Grass	Ground Team	Ground Style level 2
SetIce		Changes panels to Ice	Ground Team	Ground Style level 3
SetMetal		Changes panels to Metal	Ground Team	Under Square program shop
SetSand		Changes panels to Sand	Ground Team	NumberMan code
SetHoly		Changes panels to Holy	Ground Team	Ground style level 5
SetLava		Changes panels to Lava	Ground Team	Ground style level 4
ShdwShoe		Walk on cracked blocks without them collapsing	Guts Shadow	Shadow Style level 2
Shield		When B and left is pressed, no damage suffered	Custom Shield	Shield Style level 3
SneakRun		Weaker enemies attack less frequently.	All	Zoo Comp 3
Speed1		Megabuster fires faster	All	Start with one, Undernet 5
Speed1		Megabuster fires faster	All	Under 4, Undernet 6 BugFrag shop
Speed1		Megabuster fires faster	All	Yoka 1
SprArmor		Not pushed back when damaged.	Guts Shadow	Guts Style level 2
Tango		Heals you when low on HP (Link battles only)	All	Under Square program shop
UnderSht		If attack would normally kill you, MegaMan retains 1HP.	All	Start with it
WeapLV1		Charged Megabuster does 1 extra damage	All	NumberMan code
WeapLV1		Charged Megabuster does 1 extra damage	All	Hades Island
WeapLV1		Charged Megabuster does 1 extra damage	All	Undernet 6