I confess that I don't use bikes in their standard specification very much – although in my defence I am not the worst offender on the planet, for that Vik is an inspiration
I am constantly surprised that so many people treat a bike as a black box, something that is fixed and can't be changed. In part that is because cheap bikes are such poor value and don't last long enough to make it worth spending any money on them. Also because when you buy a cheap bike any upgrade seems expensive.
On the other hand if you buy a good bike to start with then it is going to last and last, it is going to be (much) nicer to ride and the extras won't seem so expensive (compared to the cost of the bike and also to the extra miles you will ride a nice bike).
So here are a few of my favourite upgrades of the moment.
If you have a mountain bike and do not use it on real mountains (ie your riding is on roads and Sustrans routes) then changing the tyres can give you a huge speed and comfort boost. Equally if you ride a road bike around town then fitting larger tyres can increase comfort (and puncture resistance) greatly without a huge speed cost (eg go from 23mm to 25mm or 25mmk to 28mm if clearances allow).
For example I have just switched my Mountain Bike from Kenda Tomac Nevegal DTC Tyres to Schwalbe Marathon Cross MTB Tyres. They will be nothing like as good in deep mud or loose soil, but that is not where I spend a lot of time riding. On the road the difference is obvious in noise level and speed.
When we have used mountain bikes for general purpose use and for touring we have always put on big slicks such as Continental Ultra Gatorskin MTB Tyres they make a huge difference to speed on roads as well as having much better grip (on road) than a knobbly tyres designed for mud.
I much prefer riding distances with clipless pedals and shoes (ie the shoe has a cleat that clicks onto the pedal). It is more comfortable and less tiring. But around town it is a pain to have to change into cycling shoes for every ride. I have a tried a variety of pedals with a platform on one side (for "normal" shoes, crocs, flipflops etc) and SPD the other (for longer rides). Currently my favourites (by a mile) are Shimano A530 SPD Single Sided Touring Pedals.
More to come.