Now, after finding the rear brakes stuck due to lack of cleaning and greasing I've done some work on it:

Replaced final brake lines
Replaced cylinders
Replaced brake pads

I've greased everything with copper grease and put it back together. Made sure there wasn't any air in the system and refilled the brake fluid with new stuff.
I just took her for a drive and everything seems fine. No weird noises, when I press the clutch she rolls fine. The handbrake works. She brakes fine, exept there's this vibration in the brake pedal. The faster I go, the faster the vibration gets. It was worse at the start of the drive, so it got better. I didn't drive very far of braked hard or anything. I'm also new to this stuff, so I'm not sure if this goes away of is normal after replacing brake pads. Or did I do something absolutely stupid...

Normally caused by a warped disk although I can't see why it would show itself following the work you describe. Replace a number of disks due to this and it has cleared every time.

If you have access to a dial test indicator you can check by how much although you can get a rough idea with a pencil and an axle stand

Thx. I'll have a look at the disks. Can't imagine how I'd warped them, but I'm not an expert by far. Does sound very plausible...

The commonest cause I know of is a period of heavy continous braking then holding the brake on while stationary. It causes a hot spot where the pads are clamped to the disk and uneven cooling. Use cadence braking whenever possible and get the handbrake on when stationary. If you can plan ahead it is always best to allow space to roll on for a bit when working the brakes hard.

That being said I am sure others have differing opinions

Oh, I completely second that! I'm pretty carefull, especially since in Holland we just seem to love trafficjams.

I just had a look at the disks. They are quite rusty (but still thick enough though). Probably since the car has been standing for quite a while. I think it might just be that...