What I did was add some code to my crt0.s for the irq handler. You must
write it in ARM code (.arm or .code 32). I'm not sure if you have to
save/restore registers, but I did. I call my c code interrupt handler
(which is in thumb code) to do the real stuff.

The interrupt actually happens when a timer rolls over (65535 to 0), so make
sure you enable the timer, and set the irq enable on it.

Here is some code:

#define TIMER0_IRQ 3
#define TIMER1_IRQ 4
#define TIMER2_IRQ 5
#define TIMER3_IRQ 6
#define REG_IME *(volatile uint16*)0x4000208
#define REG_IE *(volatile uint16*)0x4000200
#define REG_IF *(volatile uint16*)0x4000202
#define REG_TM0D *(volatile uint16*)0x4000100
#define REG_TM0CNT *(volatile uint16*)0x4000102
#define REG_TM1D *(volatile uint16*)0x4000104
#define REG_TM1CNT *(volatile uint16*)0x4000106
#define REG_TM2D *(volatile uint16*)0x4000108
#define REG_TM2CNT *(volatile uint16*)0x400010A
#define REG_TM3D *(volatile uint16*)0x400010C
#define REG_TM3CNT *(volatile uint16*)0x400010E
#define TIM_IRQ_ENABLE (1 << 6)


typedef struct
{
uint32 r00,r01,r02,r03,r04,r05,r06,r07,r08,r09,r10;
uint32 r11,r12,sp,lr;
}reg_list;

enabling irq for timer0
REG_IME = 0; // disable master irq
REG_IE |= (1 << TIMER0_IRQ); // enable timer0 irq
REG_TM0D = 0; // set timer 0 value
REG_TM0CNT |= TIM_IRQ_ENABLE; // make timer 0 trigger an irq, done't forget
to setup the timer and enable it
REG_IME = 1; // enable master irq

handling an interrupt (c code)
void _gba_interrupt_handler(reg_list *regs)
{
uint16 irqs = REG_IF;
uint32 set = (irqs & (1 << TIMER0_IRQ));
if(set)
{
// PROCESS INTERRUPT FOR TIMER 0 here
}

// clear irq flags
REG_IF = irqs;

// re-enable them
REG_IE |= irqs;
}

asm code for irq handling (note: it seems stmia and ldmia are broken on
Mappy):
.CODE 32
.ALIGN 2
.EXTERN _gba_interrupt_handler
.GLOBL _arm_irq_handler
.TYPE _arm_irq_handler,function

_arm_irq_handler:
@ save registers
str r0, [sp, #-4]!
str lr, [sp, #-4]!
sub sp, sp, #15*4
stmia sp, {r0 - lr}^
mov r0, sp

@ call the interrupt handler
bl _gba_interrupt_handler

@ restore registers
ldmia sp, {r0 - lr}^
mov r0, r0
ldr lr, [sp, #15*4]
add sp, sp, #15*4+8

bx lr