I've got a laptop with 32Mb ram so I want to multiboot it so I can optimize each windows for dedicated tasks.

First I installed Windows 98
Then I set BootGUI=0 in Msdos.sys so it booted to DOS
I came up with the idea of copying Windows and Program Files into a directory called Vanilla which will be the default Windows install. Then I wanted to strip Windows using 98lite to make it perform faster.
I wrote a menu for Autoexec.bat which gives you a choice of which OS to boot to. If you select 'Vanilla', it performs the attrib -s -h c: /s command and then moves Windows and Program Files from C:\OS_Store\Vanilla\ into the root of C:\ and loads it using WIN. If you select '98lite' it moves Windows and Program Files from C:\OS_Store\98lite\*.* into the root of C:\ and loads it using WIN (obviously it would move whichever OS was in the root before it moved the one you chosen). I was also going to have an Unofficial Service Pack install, a Revolutions Pack install and a Mindows install.

Of course, I was unsuccessful in moving Windows because DOS doesn't support more than 8+3 filenames. I then thought about searching for a DOS alternative which supports longer filenames but I'm bound to run into more problems.

I know there are lots of multi boot solutions but I would like to hear your thoughts.

EDIT

Ive just had an idea, I could move the program files path to windows\program files. Next, connect my laptops harddrive to my desktop computer using a 2.5inch to 3.5inch adaptor. Now, using my desktop os i can make a copy of windows and call it vanilla. Now when I put the harddrive back into my laptop I can boot to either OS by renaming an OS to windows. I can have a boot menu for this with unlimited choices of windows install.

Im sure at least one of you will find a flaw in my latest idea and tell me it wont work...

I don't get why you make it so complicated and not a dead simple multiboot with 2 or 3 partitions. Either you have your reasons or you haven't figured out an easier solution yet.
I'd make a bootable dos disk (CD or floppy depending on your laptop's hardware), and use part244.exe from "Ranish Partition Manager" on it. It's fairly easy to use.
It would alow you to create 2 primary partitions (~1,3 Gig or more for each OS) and the rest for a data partition (but keep the last cylinder for a "boot manager"). Then you install the 1st OS (or copy the files or the partition from your desktop) then make the 2nd partition active, then install the 2nd os, then using Ranish again to install the dual boot; change the MBR to "Boot Manager" and the Interface to "text", and there you go. And it's free. Don't hesitate to ask if I put you in a mess, I'll feel responsible.
Ranish can even resize your FAT32 partition.

Hey, hey, wait a minute, there are programs that allow EASILY multibooting two (or more) WIN9x's on the same partition:
http://thpc.info/dual/dualboots.html
http://thpc.info/dual/addawins.html
http://thpc.info/dual/dualwins.html

jaclaz