The people at modmyi made a fantastic list which outlines the list of compatible and non compatible apps with the iOS4.

And you can see the guide here for downgrading from iOS 4.0.2 to iOS 4.0.1, iOS 4.0, including a Jailbreaking Guide for iPhone 4, 3GS, 3G and iPod Touch.

Key :

(C) Compatible

(SC) Semi Compatible, it might cause problems when using and may not give full usage

(NC) Not compatible, it means that the apps will not be compatible at all.

20-Second Lock Screen (C)

60-Second Lock Screen (C)

3G Unrestrictor (SC) some apps don't unrestrict, like YouTube

ABGrouper (C)

ActionMenu (NC)

Activator (SC) some gestures, namely double-tap home and certain status bar gestures can have issues. Can be used to activate old popup-style iPod/media controls.

AdBlock (C)

aDownloader (SC) reboot after install

Advanced Preferences (C)

afc2add (C)

Android Lock XT (NC) cannot set lock pattern

AnyRing (NC)

AppBackup (C)

AppLinks (C)

AptBackup (C)

AttachmentSaver (NC)

Auto Shutdown (NC)

Auto Silent (C)

AVPlayer (C)

Backgrounder (SC) initial 4.0 support; specifics unknown, please try out

Battery Control (NC)

biteSMS (C)

BlankNull (C)

BossPrefs (NC)

BTstack (C) appears to be working just fine

CalendarPro (C)

CallClear (NC)

CallMe (SC) generates icons with no pictures; respring to fix

Categoreies (C)

CategoriesSB (SC) make sure to disable horizontal scrolling

Chronus (C)

Circuitous (NC)

ControlPad (C)

CrashReporter (C)

Cycorder (NC)

CyDelete (C)

Cydget (NC)

Cydia (SC) Lot's of crashes

Cyntact (SC) mixed reports, please try turning off all other extensions using SBSettings to confirm yes/no

Desktop/SMS Background (NC)

Dim Delay (NC)

dTunes (SC)

Emoji (C)

eWIFI (C)

Exchange Unlock (C)

eyeTV (C)

FakeCarrier (C)

Find In Page (NC) "SP 3.0 version" apparently works

FirewallIP (C)

Five-Column SpringBoard (NC) crashes to Safe Mode, even after uninstalling. To fix without restoring, uninstall IconSupport from Cydia

Five-Icon Dock (C)

FiveIRows (NC)

Flashlight (C)

FontSwap (SC) app works/downloads fonts, and can install all fonts EXCEPT system fonts

FrostBite (C) get from Sakurina's site, not Cydia

FullPreview (NC)

Fuzzyband (C)

gameboy4iphone (C)

genesis4iphone (NC)

GlovePod (C)

GPS Serial (C)

Grooveshark (C)

GV Mobile (C)

HapticPro (SC) all functions except keyboard taps

iBooks (C) not sure what this "issue" everyone is talking about actually is, but apparently it is fixed if you jailbreak with PwnageTool 4.1

iBlacklist (C)

iBlank (C) SpringBoard creates shadows of "nothing" underneath the blank icons, but it still works how it should

iBlueNova (NC)

iClassic (C)

Iconoclasm (NC)

Icon Harvester (NC)

IconSupport (NC) automatically installed with some SB tweaks. Must uninstall, along with the tweak itself, to get out of eternal Safe Mode

iFile (SC) some users having issues

ImaSafari (C)

iMemoryEnhancer (SC) not sure how to file this one. Some reports of phone getting completely stuck and requiring restore; others just fine

iMobileCinema (C)

Infiniboard (NC)

Infinidock (NC)

Insomnia Pro (NC)

Intelliscreen (NC)

iPhoneDelivery (NC)

iPodPop (NC)

iProtect (NC)

iRealSMS (C) beta is working

iRemix (SC) Issue with favorites

iSmartDialer (C)

iStrings (C)

iTransformToiPod (SC) breaks multitasking bar

iWep Pro (C)

iWhiteboard (C)

iWipe (C)

Jokes (C)

Kirikae (NC)

LiveClock (NC)

LockDown (NC)

LockInfo (C) works with stock plugins, Twitter, Things, WeatherIcon

Longitude (SC) appears to only update at device boot, not on intervals

LSRotator (NC)

MakeItMine (SC) fake carrier shows even in place of No Service; fake time does not work at all

Maps Enchancer (NC)

Mcleaner (C)

mAdvLock (NC)

mCoolPhone (C)

MewSeek (NC)

MiVTones (NC)

MobileFinder (NC)

MobileLog (NC)

MobileMusicPlayer Flip (NC)

MobileTerminal (SC) some say it works other say it don't

MPlayer (NC)

MultiIconRemover (NC)

MusicControl (NC) may not include status bar controls

MXTube (NC)

My3G (NC)

MyWi (NC)

nes4iphone (C)

Netatalk (C)

NESynth (C)

No Album Artwork (NC)

Notifier (NC)

OpenSSH (C)

OverBoard (NC)

Panorama (NC)

PBJ Time (C)

PdaNet (SC) Only USB works, Wi-Fi gives error

PhotoShare Web (NC)

Pirni Pro (C)

PkgBackup (C)

PogoPlank (C)

Popup Blocker (NC)

PreferenceLoader (NC) IMPORTANT NOTE: Please test compatibility with individual preference panes now that PreferenceLoader has been updated for 4.0. (version 2.0.2-1)

ProSwitcher (NC)

ProTapper (NC)

Push Doctor (NC) for this reason alone, if you rely on a hacktivated device and rely on push notifications, stay away from 4.0 for now

PwnTunes (C)

qTweeter (NC)

QuickDismiss (C)

QuickLock (NC)

QuickReply for SMS (NC)

QuickScroll 2 (SC) Crashes on triple tap

RandomRing (C)

Recent Call Log Delete (NC)

Remove Recents (C)

Resupported (NC)

RingShuffler (NC)

RMF Glebo Edition (C)

Rock (C)

roqyBT (NC)

Rotation Inhibitor (SC) may not display Photos in landscape, even if rotation is enabled

Safari Download Manager (NC)

SBRotator

SBSettings (SC) VERY mixed reports on compatibility with issues including but not limited to: can only be opened on home screen, phone toggle doesn't display icon, does not open without Activator; may crash when adjusting brightness...

SBAutolocktoggle (NC)

SBSettings Calculator Widget (C)

SBSettings Close Button Widget (C)

SBSettings Ringer/Silent Toggle (NC) shows that it is "muting" but doesn't actually work

SBSettings Syslog Toggle (C)

SBSettings UAFaker Toggle (C) resprings on toggle

SBSettings Tethering Toggle (NC)

SBSilent Toggle (NC)

SBSimplify (NC)

ScreenDimmer (C)

Screen Recorder (SC) stops recording randomly

ScreenSplitr (NC)

Scrobbl (C)

Shrink (C)

SIManager (C)

Sleep (NC)

SmartScreen (SC) mail widgets do not work

Snappy (NC)

SnapTap (NC)

SnowCover Pro (C)

SpoofFRANCE (C)

SpotBright (NC) I would stay away from this package in general since IconSupport adds the hidden icons feature into Spotlight, and dev hasn't updated it/fixed current bugs in forever

SpringBack (SC) mixed reports, please confirm either way

SpringJumps (NC)

SpringLocker (NC)

SprintBoard (C)

StatusNotifier (NC)

Stupid Laws (C)

Supreme Preferences 3.0 (SC) loads fine and most features work except for those changed by iOS 4

SwirlyMMS (NC)

SysInfoPlus (SC) Gives false information

Tab+ (C)

Tlert (NC)

ToggleSSH (C)

ToneFX (SC) works with all but MMS and Camera tones, does not shuffle ringtones

Torrentula (C)

TV Out (SC) Landscape doesn't work

Universal Search (NC)

UnlimTones (C)

UnlimVideos (NC)

USB Drive (NC)

Veency (C)

Video Recorder 3G (C)

Volume Boost (NC)

VolumeButtonExtender (NC) disables volume buttons completely

WeatherIcon (NC) crashing SpringBoard for some people when set to change icon

WiCarrier (NC)

WiFi Sync (C)

WiFiFoFum (C)

WiFiTrak (C)

WiggleFree (SC) icons wiggle until touched)

Wiimote Music Controls (C) update BTStack

Window Planar (NC)

Winterboard (SC) multitasking dock NOW FIXED, some things cannot be themed. Also, turn on SummerBoard mode for more compatibility

YFiSelect (NC)

YourTube (NC) downloads videos correctly, but only plays audio

yxFlash (NC)

This is indeed a great list compiled by the folks at modmyi and really handy to those people who have upgraded to the iOS4 and are looking for compatible applications to toy around with.

Source: Modmyi