After a certain amount of uptime (hours not days) my shortcuts and widgets take around 10 seconds to react to anything. The file browser and everything works fine once loaded so I don't think its a cpu load problem.

Any suggestions?

Sounds like it is getting paged out. Are you leaving things running in the background (daemons, browser?)

Show us what you've installed for further investigation:

I'm very OCD when it comes to my N900 and I NEVER leave anything running when im not using it, but I dont know about daemons.

3g2g-mode-selection-applet 0.4-2 user/desktop 64
accelemymote-gui 0.1.1 user/system 96
account-plugin-haze 0.7 user/network 140
adblock-plus-1.0 1maemo0-8 user/network 1548
aircrack-ng 1.0-3 user/network 1048
amazon-installer 1.0.1.1+0m5 user/other 96
an-droid-theme 1.6 user/system 10236
angrybirds 1.4.2 user/hidden 37300
ap-installer 1.0.1.1+0m5 user/other 88
bash3 3.2-0maemo10 user/utilities 520
blessn900 0.43-1 user/graphics 1740
bluetooth-dun 1.1-1 user/system 80
bounce 1.0.1 user/hidden 22036
cal-home-widget 1.0 user/desktop 160
catorise 0.8.2 user/desktop 152
cell-modem-ui 0.5.1-1 user/system 288
conky 1.6.1-0maemo5-1.1 user/desktop 680
coreutils-gnu 8.4-2maemo1 user/system 11752
countdown-home 0.7-3 user/desktop 320
custom-operator-name-widget 0.1 user/desktop 100
d-theme-futureal 1.0.0.0 user/desktop 9720
d-theme-green 1.2 user/desktop 8072
d-theme-night 1.0.0.9 user/desktop 10120
decoders-support 0.4 user/multimedia 84
drnoksnes 1.3.4 user/games 1260
dtg-installer 1.0-4.1.1+0m5 user/other 96
easy-chroot 0.3.2-1fremantle1 user/system 144
easy-deb-chroot 0.9.54-1fremantle1 user/system 2748
espeak 1.44.03 user/multimedia 48
extkbd 1.0.1 user/system 252
extmou 1.0.5 user/system 96
facebook-installer 1.0-4.1.1+0m5 user/other 88
facebook-services 0.5.5 user/hidden 52
fapman 0.6.8.1-1 user/system 828
feedservice-plugin-fb 0.5.5 user/hidden 264
feedservice-plugin-fb-common 0.5.2 user/hidden 60
feedservice2 0.5.9 user/hidden 212
flashlight-applet 0.4-4 user/desktop 248
fm-boost 0.2-2fremantle1 user/system 120
foreca-installer 1.0.1.1+0m5 user/other 88
foreca-weather-applet 0.9.5 user/desktop 816
frontview900 0.1-1 user/graphics 3919
gboggle 1.1.3maemo3-2 user/games 5200
gltron 0.70final-9maemo9 user/games 2740
grep-gnu 2.5.4-4maemo4 user/system 1116
gweled 0.4.3 user/games 840
headphoned 1.9 user/multimedia 84
hostmode-gui 0.3 user/system 188
ines 3.6.9-2 user/games 222
john 1.7.6-1 user/development 1556
kasvopus 0.9.2 user/hidden 320
kernel-power-flasher 2.6.28-maemo46-wl1 user/system 236
kernel-power-settings 0.11 user/system 140
kroll 1.3.4 user/hidden 97295
leafpad 0.8.17le-0maemo1 user/utilities 944
led-pattern-editor 0.0.4-1 user/system 188
libqtm-bearer 1:1.0.2-maemo4+0m5 user/libs 300
libqtm-contacts 1:1.0.2-maemo4+0m5 user/libs 1012
libqtm-location 1:1.0.2-maemo4+0m5 user/libs 256
libqtm-messaging 1:1.0.2-maemo4+0m5 user/libs 848
libqtm-multimedia 1:1.0.2-maemo4+0m5 user/libs 1544
libqtm-publishsubscribe 1:1.0.2-maemo4+0m5 user/libs 244
libqtm-sensors 1:1.0.2-maemo4+0m5 user/libs 336
libqtm-serviceframework 1:1.0.2-maemo4+0m5 user/libs 392
libqtm-systeminfo 1:1.0.2-maemo4+0m5 user/libs 420
libqtm-versit 1:1.0.2-maemo4+0m5 user/libs 468
lzma 4.43-14maemo5 user/utilities 164
macchanger 1.5.0-3 user/network 316
maemo-org 2.0.1-9 user/desktop 11516
mobilehotspot 0.3.4 user/network 192
mp-fremantle-203-pr 20.2010.36-2.203.1 user/system
mupen64plus-arm-gui 20100929-0maemo1 user/games 68
n900-fmrx-enabler 1.5-4+0m5 user/libs 92
nehegles 1.4.1 user/development 1952
njurassiclite 1.0.1 user/hidden 34100
nspeed 1.2-2 user/games 1192
ogg-support 1.0.5 user/multimedia 136
omnom 0.2.4-0 user/games 1260
openarena 0.8.1-maemo1 user/games 2912
personal-gprs-mon 0.6-3 user/desktop 292
petrovich 0.2 user/system 76
picodrive 1.32-1 user/games 960
proximityd 0.2.2 user/system 88
purple-extra-protocols 2.7.3-0nix2 user/network 180
pygtkeditor 3.0.19-1 user/development 608
python2.5-qt4 4.7.5-maemo2 user/development 36
qtirreco 0.3.0-1 user/utilities 1776
queen-beecon 1.2 user/desktop 464
recaller 2.0.0-7 user/desktop 176
recovery-tools 6.11-9-fremantle5 user/utilities 772
rootsh 1.5 user/system 32
seriesfinale 0.6.5-1 user/utilities 324
sharing-service-facebook 0.5.1 user/hidden 184
shortcutd 0.1.3-2 user/system 240
simple-brightness-applet 1.1-1maemo0 user/desktop 64
sixad 1.3.0-0maemo2 user/system 424
sixaxis-support 1.2-2 user/system 28
smsbomb 0.2.1-1 user/network 112
smssend 0.1.6 user/utilities 84
starhash-enabler 0.2 user/system 16
ttf-droid 1.01-dfsg0maemo3 user/graphics 4392
tutorial-home-applet 0.6.16+0m5 user/support 1292
tweakflashver 0.4.0-maemo1 user/utilities 212
tweakr 0.0.17-2 user/system 228
vgb 3.5.6-2 user/games 241
vgba 3.6.8-2 user/games 418
vncviewer 0.6.5-fremantle4 user/network 224
wifi-switcher 0.0.6 user/desktop 140
zenbounddemo 1.0.6-1 user/hidden 13

just reboot
it always happens to me

Rebooting wastes time, and battery charge, it would be better to find a solution that actually fix the issue instead of just sweeping things to under the rug.

I find the same thing happens to me but usually after 2+ days of uptime. I try and keep it going but after 4 days it becames very tiresome.
A reboot isnt an option when you are out and a reboot will consume about 25% battery (which it does sometimes).

Try to remove catorise app - there were some similar problems with it (at least with PR1.3)

@FRuMMaGe you don't need petrovich neither, as its function is available after PR1.2.

Also, the following might be the cause of the stability issues and you'd like to remove them and test:

proximityd
recaller

Do remove catorize. Does wonders to your battery life if nothing else.